diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000001_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000001_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d599a28bde23247e55ed17534b2b008b5faa2393
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000001_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000002_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000002_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d28467da04259763d06fa23da2142f9e685d865c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000002_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000008_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000008_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0eb6ef75c608d925e0794c10c85eb79ef5e4604
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000008_tree_id.txt
@@ -0,0 +1 @@
+(0_2166:0.026190977,(4_971:0.0,4_1111:0.0):0.003732667,((0_685:0.0,1_80:0.0,1_327:0.0,1_974:0.0,1_1350:0.0,1_2226:0.0,4_581:0.0,4_1300:0.0,4_2104:0.0):0.000000005,(0_1350:0.071903674,(0_1449:0.004437045,0_2164:0.467930074)0.669:0.002440869)0.971:0.062143573)0.000:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000009_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000009_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7aceba8116ae9682f4aa9e3df4116a8719dd687
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000009_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000010_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000010_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e085b1d4517b5f34e91779b8f1dd3b85577e233
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000010_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000011_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000011_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..894c670ae5c26058181c1dff683fe1b179e34e4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000011_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000013_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000013_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b00073928043b866c283afcfea63a30f04143d97
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000013_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000015_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000015_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb717e82dbc0c8e4145735813951d3288c1c5a7b
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000015_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000016_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000016_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e5b67f1db0a50561bd118ac8ca301a76be8f399
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000016_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000017_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000017_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c826dc431efc068b5dd864480004e3690823cf9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000017_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000018_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000018_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4f702ccf99c5a4e897ac9314f74c2a66aec803d
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000018_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000022_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000022_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a194940fb247cde5bb015926aea87cd9d60ea0bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000022_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000023_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000023_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4379f5625fad5fb204c34edc64f6751a3c245878
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000023_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000024_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000024_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6bb8307a2a8ea08eb11d746d0f807d699bc7c11
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000024_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000026_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000026_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5684aa35025c4d780d44afd79c3dfd5996091145
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000028_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000028_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fef7916fc1115c055d068b5c4741f0431c315a14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000028_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000031_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000031_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18f9ecae68b778fd0fb98ffa0b27c104ae2df764
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000032_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000032_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..177801df40326cd5213031b8500cb7504f3026e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000032_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000033_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000033_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db105371869b239042fa579397fd0c2ff9695e36
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000033_tree_id.txt
@@ -0,0 +1 @@
+(0_251:0.000000005,4_249:0.004529161,(1_2215:0.006200038,(2_100:0.168365538,(3_68:0.322084255,(2_572:0.963637019,3_507:1.110253120)0.971:0.344305053)0.999:0.370411442)1.000:0.228559943)0.831:0.007530464);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000034_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000034_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b5a0f597da0a0daf0c3e602ef16a6b50b7a6175
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000034_tree_id.txt
@@ -0,0 +1 @@
+(2_700:0.008483740,((0_592:0.0,0_2014:0.0):0.005075056,1_1730:0.000000005)0.832:0.007066105,((1_324:0.0,3_2162:0.0):0.015427088,4_1943:0.198197716)0.267:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000035_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000035_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64e75decbbd6872ae20514dbdcf5e90113ed5019
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000035_tree_id.txt
@@ -0,0 +1 @@
+(0_602:0.010135620,(1_356:0.0,4_579:0.0):0.000000005,(3_2137:0.051833311,(2_394:0.000000005,(2_373:0.000000005,2_377:0.030262711)0.834:0.010151309)0.580:0.010108217)0.821:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000038_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000038_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..764623401dded832ccc86e86b0cb9e6a2b334051
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000038_tree_id.txt
@@ -0,0 +1 @@
+(1_1437:0.009752907,4_1649:0.004148329,(0_1720:0.002131851,(3_1003:0.090621132,(2_1078:0.062421825,(0_806:0.127971011,0_807:0.059039245)0.477:0.526808430)0.869:0.045687183)1.000:0.062472050)0.440:0.003476338);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000039_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000039_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e22b49678a3945deaa94749836165b364e12c58
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000039_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000041_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000041_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..af1da8c9732b85ff77e0dd0d9a3c94ab42383f5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000041_tree_id.txt
@@ -0,0 +1 @@
+(0_1134:0.005291202,4_1084:0.005235306,(1_862:0.008373669,(2_1678:0.366496538,(2_1677:0.254724526,(3_300:0.937968762,3_1575:0.464667982)0.922:0.162915885)0.769:0.078972292)0.760:0.053175892)0.766:0.004929119);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000044_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000044_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44182b8a9cf6b535392b8fa1294ec6e89cac63c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000044_tree_id.txt
@@ -0,0 +1 @@
+((2_397:0.025161344,(1_1092:0.000000005,4_1302:0.053372627)0.805:0.007166293)0.748:0.003466790,(3_632:0.0,3_2165:0.0):0.000000005,(0_1353:0.111216408,3_312:0.084218618)0.749:0.002727010);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000046_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000046_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52d73c02aad087ad37926736ece4d96b447425cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000046_tree_id.txt
@@ -0,0 +1 @@
+(0_1986:0.003453929,4_1921:0.000000005,(1_1703:0.008217784,(3_715:0.256468139,(3_725:0.372275135,(0_1732:0.006840987,2_1064:0.000000005)1.000:0.667737676)0.946:0.181765391)0.999:0.195326962)0.903:0.019789870);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000047_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000047_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ddf6715c12eadfc6f570b26d50e6efafc8de2cb9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000047_tree_id.txt
@@ -0,0 +1 @@
+(0_1747:0.006651265,4_1669:0.000000005,(1_1455:0.038318586,(2_1047:0.056251453,(3_983:0.105961576,(2_381:0.217562705,2_2582:0.804782208)0.976:0.171489140)0.998:0.101922158)0.973:0.045716402)0.909:0.017337170);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000049_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000049_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e04041366f035b8fd5005a71547bc00397b83b7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000049_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000050_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000050_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75b7049d3e9efdfe88e9c32c031f0b30af86f306
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000050_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000051_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000051_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..081127c5ffe4f242736ad7c5daa4a030a33fa7b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000051_tree_id.txt
@@ -0,0 +1 @@
+(0_2033:0.040989379,2_666:0.038751200,((1_1752:0.000133362,3_583:0.066633616)0.596:0.017847017,((3_2050:0.508887497,4_1971:0.613186748)0.994:0.624215157,3_582:0.111869333)0.449:0.026364296)0.747:0.013371747);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000054_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000054_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91b37b008728c535216f5c037ccd56ac38979dee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000054_tree_id.txt
@@ -0,0 +1 @@
+(0_2192:0.007127824,1_1902:0.003003070,((2_470:0.016182436,(4_2124:0.004031907,3_417:0.006076333)0.735:0.001997491)0.866:0.006104434,(0_2214:0.289689808,2_475:0.173257320)0.933:0.157487082)0.756:0.001857403);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000055_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000055_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a8147c37be55186abc07efcac403df31e8c3ee5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000055_tree_id.txt
@@ -0,0 +1 @@
+(2_989:0.469058988,3_851:0.717823672,(3_923:0.492378277,(4_708:0.225294060,(3_774:0.083699701,(1_1646:0.013957249,2_836:0.006234928)0.997:0.122743158)0.993:0.231848900)0.998:0.350521709)0.826:0.105665103);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000060_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000060_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a4d52bb4a067455358ae1b4e1a223d09fe1292b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000060_tree_id.txt
@@ -0,0 +1 @@
+(0_59:0.003429734,1_2023:0.027149516,(4_54:0.016550537,(2_191:1.781957831,(3_259:0.128202971,2_317:0.101312677)0.000:0.000000005)0.973:0.138072217)0.655:0.008055982);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000061_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000061_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62c0ababbf010b2cfc74bc254c78cadea9c427cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000061_tree_id.txt
@@ -0,0 +1 @@
+(0_64:0.000000006,1_2028:0.010665523,(4_58:0.005318665,(2_311:0.075952761,(3_252:0.050777832,3_667:0.781922302)0.769:0.029282341)0.933:0.034351470)0.688:0.006505499);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000066_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000066_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37bad58692714cc5a8d490217a5b267bf0c04a5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000066_tree_id.txt
@@ -0,0 +1 @@
+(0_190:0.003311563,3_139:0.000000006,(4_190:0.016621484,(1_2137:0.010156763,(1_1974:1.432226735,2_187:0.150655186)0.965:0.217831028)0.793:0.006432267)1.000:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000068_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000068_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6f768f7ef6cbc3d8ecb92dac4a6ba025cd50617d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000068_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000072_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000072_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52b7b8fd9d604bb59e7e4a0fe738b6244449f6cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000072_tree_id.txt
@@ -0,0 +1 @@
+(1_2204:0.004917749,4_241:0.001852616,(0_241:0.006171009,(2_111:0.030119593,(3_79:0.078141714,3_2414:0.394103166)1.000:0.097101257)0.993:0.034630196)0.787:0.007829956);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000077_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000077_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9fb7f11912b8dc74b8fe0d006c2da252179b25e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000077_tree_id.txt
@@ -0,0 +1 @@
+(0_286:0.013001028,4_293:0.008711931,(1_3:0.033880200,(2_50:0.086068837,(3_28:0.090842194,3_1198:2.016793608)0.843:0.116044216)0.965:0.059405261)0.978:0.029602788);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000078_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000078_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..636c63333b5418b884d4fd5b9c0fa2efe0ea6f47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000078_tree_id.txt
@@ -0,0 +1 @@
+(1_21:0.005596494,4_304:0.000000005,(0_297:0.002910690,(3_637:1.322455078,(2_22:0.244169503,3_18:0.194341570)0.885:0.073014270)0.931:0.103671235)0.878:0.011243791);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000081_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000081_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d6801e2ef7927bc9980d68710b810872b576acd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000081_tree_id.txt
@@ -0,0 +1 @@
+(1_71:0.001540960,4_353:0.001541832,(0_346:0.004574970,(2_2538:0.041689999,(2_183:1.165161959,3_2397:0.063052357)0.892:0.048328693)0.968:0.019963277)0.858:0.003164498);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000082_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000082_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2cec26cda6d2e1a5c6b9b45eb5bc691e6f00f740
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000082_tree_id.txt
@@ -0,0 +1 @@
+((4_371:0.006630660,(0_365:0.000000005,1_98:0.003468872)0.875:0.003799427)0.848:0.003611571,3_2388:0.034183912,(2_2513:0.029265872,3_1719:0.096210331)0.446:0.005737323);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000084_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000084_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..662308b625b970bccd6a6aa27372b75fdb0eb178
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000084_tree_id.txt
@@ -0,0 +1 @@
+(0_397:0.000000005,4_400:0.001733995,(1_127:0.056171871,(2_2485:0.230212077,(2_2486:0.663339006,3_2354:0.831313542)0.999:0.356889250)0.792:0.072365415)0.951:0.032579821);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000085_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000085_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d0fce5d84b676c8cefd68016f9ab660aa255515a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000085_tree_id.txt
@@ -0,0 +1 @@
+(1_132:0.011873847,4_405:0.006222400,(0_402:0.016594706,(2_2478:0.096929533,(3_2349:0.105028646,2_2479:0.101282615)0.661:0.018405652)0.995:0.078216636)0.916:0.011001015);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000086_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000086_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..531984d36f869174c09cbf67e602484f9363cb79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000086_tree_id.txt
@@ -0,0 +1 @@
+(0_427:0.000000005,1_157:0.002331144,((2_2453:0.034717800,3_2324:0.065699661)0.998:0.038426227,(3_666:0.970279730,4_430:0.002324367)0.000:0.000010643)1.000:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000088_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000088_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db7875d1f80f86bd73cd7c050a0bddfe5f86493e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000088_tree_id.txt
@@ -0,0 +1 @@
+(2_2398:0.030372847,4_472:0.020253200,(0_473:0.009171435,(1_203:0.000000005,(2_1196:1.416792867,3_2281:0.102928431)0.949:0.185651102)0.851:0.011216223)0.574:0.004948185);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000091_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000091_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a60a86cf6e598f03f306eead251e1ceda4afc118
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000091_tree_id.txt
@@ -0,0 +1 @@
+((2_2346:0.075752697,(2_2347:0.146036538,3_2230:0.417017257)0.913:0.125162743)0.955:0.078889760,0_524:0.003784506,(4_527:0.007117166,1_258:0.010619101)0.763:0.003283313);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000095_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000095_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8dba80b69df6926947c32c8af315ae6f05165f64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000095_tree_id.txt
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+(0_586:0.133728598,(1_311:0.0,4_1948:0.0):0.068204313,(3_1166:1.394821723,(1_1721:0.289777768,2_2293:0.102409445)0.699:0.035200777)0.615:0.015654377);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000097_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000097_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b76af89ec5a285e3080827677482dd26f52f2592
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000097_tree_id.txt
@@ -0,0 +1 @@
+(3_2159:0.044301346,(1_345:0.036354026,2_1285:0.060542884)0.392:0.016198587,(0_595:0.027893804,(3_672:0.050454935,3_2163:1.268604741)0.000:0.000000005)0.595:0.004791247);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000098_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000098_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9036263c88c178d4ddc162df5c00007fbfe0dff4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000098_tree_id.txt
@@ -0,0 +1 @@
+(1_355:0.003387910,4_580:0.006820107,((2_376:0.000000005,2_395:0.047737643)0.911:0.013652555,(0_601:0.126624120,3_2136:0.036623387)0.834:0.008657013)0.957:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000102_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000102_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03abb2852faeda20f667f1d3834e75dfdbaa9a04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000102_tree_id.txt
@@ -0,0 +1 @@
+(0_630:0.000000005,4_600:0.003549917,(1_376:0.000000005,(3_2113:0.245887629,(2_152:1.393793085,2_2257:0.057283058)0.804:0.043512808)0.842:0.021580371)0.844:0.003548822);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000104_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000104_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4489b437b545872a33e6392f1620eaaa23813e0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000104_tree_id.txt
@@ -0,0 +1 @@
+(0_705:0.001873356,4_669:0.002822145,(1_445:0.015879603,(2_2172:0.175407280,(3_328:1.429674489,3_2047:0.305460937)0.999:0.309240303)1.000:0.157637164)0.910:0.013167251);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000106_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000106_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6cc329f312fa4d3f330e74fa8804d31ec635df4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000106_tree_id.txt
@@ -0,0 +1 @@
+(0_735:0.007317146,1_474:0.003600657,(4_699:0.000000005,(2_2119:0.199679637,(3_511:1.676124975,3_2013:0.085618502)0.841:0.105368726)1.000:0.208995759)0.937:0.014716013);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000107_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000107_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..920fcb7f96c50330f35914d87fcc57f466bbf92f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000107_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000109_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000109_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db5ea0acd0609d2514c5bca392afc33eb397ec23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000109_tree_id.txt
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+(3_1902:0.363455955,(2_2009:0.004636088,4_809:0.007032620)1.000:0.281194667,((0_853:0.0,1_584:0.0):0.298792180,2_2007:1.391981961)0.991:0.194170577);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000110_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000110_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..82c7718f85abc8a0a786e46907a861c0e3c337d1
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000114_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000114_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1aec0c2cf9ecc6fb8b931130ef90190bda9929d7
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000116_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000116_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ec540477384d215393cfecf1184d3fd05e57719
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000117_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000117_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2311d12c5ea08d2f678105ff639d1ffbae209750
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000128_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000128_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78d8db540bbeb1cca6b69ae2233162d3fb2393b0
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000130_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000130_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a7bfd3d7035882965912b09c7174d28bce67dcb
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000134_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000134_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58311c1c7876e059758244ef08933cc397deeafb
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000136_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000136_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e5ab4260b034b6d3e83222e0c592ef762803240
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000138_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000138_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5860c3c0369f7daae570a7cc9a100ba2c0273fe8
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000138_tree_id.txt
@@ -0,0 +1 @@
+(0_1547:0.007300830,(1_1269:0.0,4_1474:0.0):0.007294008,(3_1177:0.000000005,(3_257:1.763513679,3_1785:1.682650899)0.537:0.017465668)0.648:0.018304188);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000140_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000140_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f9bb3d9b3346b55a13c47e7c319901e7e539eec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000140_tree_id.txt
@@ -0,0 +1 @@
+(0_1570:0.000000005,1_1286:0.004933047,((3_763:1.696835684,2_1248:0.000000005)0.416:0.005186133,(3_1158:0.000000005,4_1497:0.017434298)0.482:0.002906839)0.372:0.002704461);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000145_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000145_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee8bb4dc9c7c3a60a201c747e474dd3b5c3a71ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000145_tree_id.txt
@@ -0,0 +1 @@
+(((0_1731:0.0,2_1065:0.0):1.033186538,3_711:0.482982880)0.850:0.151109413,4_1925:0.011849579,(1_1707:0.014709265,0_1990:0.000000005)0.408:0.002856633);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000146_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000146_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88cd41b9e1d589138b31fce74c1bfd210ad831dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000146_tree_id.txt
@@ -0,0 +1 @@
+(1_1706:0.001802687,4_1924:0.005412016,(0_1989:0.005811325,((0_1736:0.0,2_1060:0.0):0.701311151,3_712:0.144457646)1.000:0.288636225)0.746:0.005063524);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000147_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000147_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6b53fc805ec4b9337aed350c15f4625e1ec451ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000147_tree_id.txt
@@ -0,0 +1 @@
+(2_1044:0.050136823,((0_1750:0.0,1_1458:0.0):0.007374408,4_1672:0.015606325)0.990:0.071464576,(2_2585:0.967375712,3_980:0.123959242)0.830:0.052977082);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000148_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000148_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..af5ef2dc934c0fac7fd3165ccecaf07398e112dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000148_tree_id.txt
@@ -0,0 +1 @@
+(0_1771:0.007394383,1_1479:0.012495504,(4_1693:0.016209160,(2_1017:0.149934328,(2_726:0.533325942,2_2284:1.566714421)0.342:0.106927212)0.987:0.117802860)0.743:0.003742410);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000152_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000152_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a99b147e62c14759f482cf334c749ec386a37879
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000152_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000154_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000154_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e95bc61db1881ec1e31da14fd55bf85fed2ba51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000154_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000155_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000155_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4c3ee87825e77c7509597796ad0030ca7fc620f
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000155_tree_id.txt
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+(3_790:0.014448645,(1_1629:0.004792401,0_1924:0.019219049)0.236:0.004755915,(4_1851:0.000000006,(2_853:0.124314499,3_800:0.170247570)0.997:0.121846264)0.000:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000157_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000157_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b58ffe90a762098fb10d78fbde573d000178408
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000157_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000159_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000159_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58a2b60af16ed0a041bce8f82d009abeb9e71a6f
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000159_tree_id.txt
@@ -0,0 +1 @@
+((1_1068:0.842665901,3_469:0.357711553)0.926:0.193150948,(0_2009:0.000000005,4_1938:0.015471112)0.978:0.205072257,(2_542:0.306316454,2_725:0.097102533)0.736:0.066294857);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000160_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000160_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2516813664accfbcad5ab3b465cc8aa4a899e295
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000160_tree_id.txt
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+(2_722:0.197833605,3_471:0.193000468,(2_718:0.400108501,(2_723:0.166296532,(0_2011:0.052786365,4_1940:0.000000005)0.965:0.207809970)1.000:0.578075997)0.926:0.192612760);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000165_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000165_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bbf3c08f95cb3641688d2d664976e8a0dce78c8b
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000165_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000166_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000166_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c61f89eb62168ce97104e4ea9b78ef9801541d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000166_tree_id.txt
@@ -0,0 +1 @@
+(0_2107:0.018521059,4_2053:0.012481936,(1_1832:0.006543865,(2_566:0.090165043,(3_493:0.165769513,3_1863:1.710802884)0.228:0.065884918)0.886:0.060875671)0.748:0.005733560);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000167_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000167_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3764962f038e24bce3827e12a37e22e5f138f17
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000167_tree_id.txt
@@ -0,0 +1 @@
+(0_2123:0.000000005,4_2069:0.003710495,(1_1848:0.006348780,(2_548:0.070398375,(3_474:0.193376987,4_158:1.461543142)0.706:0.042259322)0.983:0.035908496)0.775:0.004988325);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000168_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000168_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c32466a7cbe85f1a22447d03d08403e4171099d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000168_tree_id.txt
@@ -0,0 +1 @@
+(2_471:0.049511164,(0_2191:0.005638319,0_2215:0.017035499)0.770:0.002861985,(3_418:0.008490245,(1_1901:0.005641886,4_2123:0.000000006)0.776:0.005659257)0.757:0.002794306);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000169_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000169_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..603f98e50d9cf4f3eac5d799c5bcdaae0702c09a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000169_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000170_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000170_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..087b88f3f4e908147935c1fdb6bacb7f69b07bde
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000170_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000173_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000173_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..006e83e461cae0ea5f16712e801b025e9869e2b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000173_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000175_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000175_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ed9a532d7d09773bd03be42de4bbed62f810d5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000175_tree_id.txt
@@ -0,0 +1 @@
+((0_1:0.0,1_1957:0.0,4_1:0.0):0.024147308,2_404:0.017167948,3_358:0.114544741);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000176_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000176_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c62dbbef99583f1c8c79df576d4840f817e7bf5
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000177_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000177_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d92cba82d491f0ecd582c70b43c11662ed97c353
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000179_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000179_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fae6851833d42e23baf999b0db45dcf059f61f0a
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+(0_5:0.002291805,4_5:0.000000005,(1_1961:0.001101731,(2_400:0.021507603,3_353:0.086957853)0.999:0.024556251)0.360:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000180_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000180_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0649805722db8b4de2ee1390c408c1d9c7debd3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000180_tree_id.txt
@@ -0,0 +1 @@
+(0_6:0.000000005,(1_1962:0.0,4_6:0.0):0.005712763,(2_399:0.059330832,3_352:0.248918950)0.990:0.098243938);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000181_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000181_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a1c7d45033c41b913ef05b9138d10a0a497bc972
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000181_tree_id.txt
@@ -0,0 +1 @@
+(0_7:0.018327207,(1_1963:0.0,4_7:0.0):0.000000006,(2_398:0.063359609,3_351:0.691254863)0.883:0.097936239);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000183_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000183_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40cbea6c4fd0fee2a56f63989cc754027d7e19cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000183_tree_id.txt
@@ -0,0 +1 @@
+(0_11:0.002423224,4_11:0.002362262,(1_1980:0.011693569,(2_367:0.131603004,3_349:0.599494759)0.991:0.131452773)0.854:0.013116716);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000184_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000184_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa5b88efd88a9d5fc65c50529e14d07796849952
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000184_tree_id.txt
@@ -0,0 +1 @@
+((0_12:0.0,1_1981:0.0,4_12:0.0):0.045650185,2_366:0.033180536,3_348:0.024837458);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000185_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000185_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..76e991ff8fc9d99bfc56932ee023a8d8fdc1a6a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000185_tree_id.txt
@@ -0,0 +1 @@
+(0_13:0.006488304,4_13:0.009632845,(1_1982:0.018935911,(2_365:0.220099155,3_347:0.333855061)0.965:0.078673807)0.597:0.000965236);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000186_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000186_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d41933e822cb9e002500f8a86a4e932dcb974518
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000186_tree_id.txt
@@ -0,0 +1 @@
+(0_14:0.010275258,1_1983:0.010357015,(4_14:0.000000005,(2_364:0.063982042,3_346:0.230797707)0.868:0.051050599)0.000:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000188_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000188_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ec2cb0853af8c3ed94c1cdf754549dcfa2a0b67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000188_tree_id.txt
@@ -0,0 +1 @@
+(0_16:0.010088452,4_16:0.026125830,(1_1985:0.026368367,(2_361:0.220339480,3_344:0.605618374)0.995:0.157110100)0.477:0.006663358);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000189_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000189_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15553ca21b35787946d8109c2602646dbcc9260c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000189_tree_id.txt
@@ -0,0 +1 @@
+(1_1986:0.011443078,4_17:0.010782256,(0_17:0.006532447,(2_360:0.116401153,3_343:0.343021829)0.988:0.071633501)0.963:0.018084828);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000196_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000196_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..393f36ef56be9368b65795e71f344a527b7ebddd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000196_tree_id.txt
@@ -0,0 +1 @@
+(0_30:0.005295389,1_1998:0.000000005,(4_29:0.005336118,(2_347:0.063847547,3_289:0.079628149)0.981:0.044506198)0.732:0.005290355);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000198_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000198_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6be7442e00b901f033e1cc510f52ddb9dc152e97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000198_tree_id.txt
@@ -0,0 +1 @@
+(0_35:0.000000005,1_1999:0.004234729,(4_30:0.008623286,(2_346:0.095951560,3_288:0.054575523)0.970:0.050246776)0.844:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000199_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000199_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ce5b2ff150f8d23004f090a1306c5971e3b13f8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000199_tree_id.txt
@@ -0,0 +1 @@
+(0_36:0.006480548,4_31:0.009835063,(1_2000:0.003474834,(2_345:0.109714930,3_287:0.250064504)0.988:0.096035422)0.815:0.006292622);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000205_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000205_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd73f6ab2b5b907e179ad11b75c6102f5083fb64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000205_tree_id.txt
@@ -0,0 +1 @@
+(1_2007:0.010404419,4_38:0.017401012,(0_43:0.010801905,(2_333:0.193745613,3_281:0.484951744)0.999:0.195258655)0.590:0.010592373);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000207_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000207_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f74266c50ba90ebcae4a24cc6cba194c6e953cdd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000207_tree_id.txt
@@ -0,0 +1 @@
+(2_329:0.114344720,4_45:0.008203486,(0_50:0.002225727,(1_2014:0.004229456,3_268:0.015957348)0.687:0.004012886)0.789:0.003629954);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000208_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000208_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b559c4a8a5addb967d5b844a5e0458618d8b66b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000208_tree_id.txt
@@ -0,0 +1 @@
+(0_51:0.006929749,4_46:0.000000005,(1_2015:0.000000005,(2_327:0.026524615,3_267:0.104234790)0.999:0.047600865)0.750:0.003455967);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000209_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000209_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a32664bd1e6dbfbe98330016ddd19757c59e94d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000209_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000210_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000210_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d847913ec1ecdbb63eba31915f6dacd41a2faa07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000210_tree_id.txt
@@ -0,0 +1 @@
+(0_53:0.002683605,4_48:0.002678257,(2_323:0.135538943,(1_2017:0.002987781,3_264:0.385463976)0.084:0.002484317)0.778:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000211_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000211_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06e3290a9b71fd8c71c586e999a6cdcd79c31928
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000211_tree_id.txt
@@ -0,0 +1 @@
+(1_2018:0.005624198,4_49:0.001402122,(0_54:0.007800264,(2_322:0.057525181,3_263:0.334820419)1.000:0.079592413)0.746:0.002033064);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000212_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000212_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54a82c04b7bd232b63eed541167daf3a43ec4e65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000212_tree_id.txt
@@ -0,0 +1 @@
+(1_2020:0.019509434,4_51:0.003838260,(0_56:0.000000005,(2_320:0.088308395,3_262:0.314204471)0.997:0.083191971)0.325:0.003880105);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000213_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000213_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dda445d17e1ce3d5c46f6cad66932e0935516076
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000213_tree_id.txt
@@ -0,0 +1 @@
+(2_319:0.018759639,3_261:0.069844280,((0_57:0.0,4_52:0.0):0.000000005,1_2021:0.009327532)0.917:0.029238199);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000215_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000215_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b1d862a8a1e02a07417d9460ccfd3db4a8490577
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000215_tree_id.txt
@@ -0,0 +1 @@
+(0_61:0.011571252,4_55:0.004767253,(1_2025:0.004786674,(2_315:0.045598039,3_258:0.115739505)0.980:0.029538906)0.405:0.002333351);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000218_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000218_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e3be35997b03c581a138c60774897e97bfe31cc4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000218_tree_id.txt
@@ -0,0 +1 @@
+(0_65:0.016086339,4_59:0.009967415,(1_2029:0.017260428,(2_308:0.339084290,3_251:0.294212343)1.000:0.207267483)0.798:0.009246487);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000221_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000221_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14cb4799fde44a3c18b925244c6bd3dbb91c5f9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000221_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000222_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000222_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..71a5def2b933042811eabb85483f364329fcdd17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000222_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000225_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000225_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30ab67fa019f83bd06ec14ee056df6c4298b2c21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000225_tree_id.txt
@@ -0,0 +1 @@
+(0_74:0.016160617,(1_2038:0.0,4_68:0.0):0.016553016,(2_300:0.072015297,3_242:0.362368593)0.973:0.102897658);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000228_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000228_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5bc508374faaf315aa93eea9fbd19e9e51d26d61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000228_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000230_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000230_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f21e3518bac45da091e858ba876aeb2489cddc74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000230_tree_id.txt
@@ -0,0 +1 @@
+(0_80:0.020485996,(1_2044:0.0,4_75:0.0):0.007120585,(2_292:0.112751671,3_237:0.515325252)0.201:0.049450634);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000231_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000231_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..969977eefda5e22249aa33b19918cec78f638c93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000231_tree_id.txt
@@ -0,0 +1 @@
+(3_236:0.519353936,(1_2046:0.002381232,4_77:0.000000005)0.905:0.016868922,(2_290:0.036170152,0_82:0.008187604)0.637:0.005008213);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000234_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000234_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1c946de54c63f132bffeb61f40b605e0c138a6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000234_tree_id.txt
@@ -0,0 +1 @@
+(0_85:0.008262122,1_2049:0.000000005,(4_80:0.004642243,(2_287:0.081718644,3_233:0.311293513)0.998:0.134772831)0.832:0.016124156);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000241_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000241_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e50e32613b8549575a047748b97af3d362299a3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000241_tree_id.txt
@@ -0,0 +1 @@
+(1_2056:0.000000005,4_87:0.002994485,(0_92:0.005342346,(2_280:0.118440870,3_226:0.112261928)0.997:0.077793955)0.863:0.009657965);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000244_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000244_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49e25ec00eb287ce672e7ac5ab49e429978a485f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000244_tree_id.txt
@@ -0,0 +1 @@
+(0_96:0.001168048,4_91:0.000000005,(1_2060:0.002341415,(2_276:0.017190620,3_223:0.051045688)0.972:0.009774257)0.781:0.001166601);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000245_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000245_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8649c889a3e52d08641d2f04ba3d845df8d257d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000245_tree_id.txt
@@ -0,0 +1 @@
+(1_2061:0.000000005,(2_274:0.000000005,3_221:0.384873880)0.936:0.049876289,(0_97:0.000000005,4_92:0.016285411)0.922:0.016190048);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000247_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000247_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ee7e308ce3a5fe880492f0e8a85bde8c93ff6dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000247_tree_id.txt
@@ -0,0 +1 @@
+(1_2063:0.003246185,4_94:0.012935364,(0_99:0.010078049,(2_272:0.045488941,3_219:0.202239447)0.999:0.104234132)0.812:0.006060980);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000248_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000248_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86f5ea1e53d7f7658f7d48af1c558dbc4afd8427
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000248_tree_id.txt
@@ -0,0 +1 @@
+(4_95:0.000000005,(2_271:0.155975944,3_218:0.561218554)0.998:0.172312041,(1_2064:0.006919359,0_100:0.013871927)0.909:0.017570299);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000249_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000249_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ad12f4808e1007ffd1880f131d34a083ca22dec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000249_tree_id.txt
@@ -0,0 +1 @@
+(0_102:0.007565697,4_97:0.000000005,(1_2066:0.000000005,(2_269:0.082851740,3_211:0.204708145)1.000:0.093373282)0.240:0.010063911);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000250_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000250_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..04168cba2c0dcba810255a9c34c78d17019c20af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000250_tree_id.txt
@@ -0,0 +1 @@
+(4_98:0.007501844,(2_268:0.070152134,3_210:0.315816909)1.000:0.176121990,(0_103:0.000000005,1_2067:0.002528577)0.562:0.000360940);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000251_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000251_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0cc796cba9668230124ec17793a278e3161c31c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000251_tree_id.txt
@@ -0,0 +1 @@
+(2_267:0.102019675,3_209:0.056776847,((0_104:0.0,1_2068:0.0):0.003101598,4_99:0.000000005)1.000:0.169610808);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000252_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000252_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d0f85a916623c9fc6896d46ccbe31005488e8724
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000252_tree_id.txt
@@ -0,0 +1 @@
+((0_105:0.0,1_2069:0.0,4_100:0.0):0.229648804,2_266:0.128524656,3_208:0.117121639);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000257_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000257_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd03bde7f330544f52b33ea521699c23368bfff4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000257_tree_id.txt
@@ -0,0 +1 @@
+((0_110:0.0,1_2074:0.0):0.004268275,4_115:0.004009116,(2_258:0.097480672,3_191:0.159622154)0.991:0.089998962);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000258_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000258_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..896c3b1fa3bbb0bebff2502cfdf65659b2c561b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000258_tree_id.txt
@@ -0,0 +1 @@
+((2_257:0.094722074,3_190:0.389815799)0.995:0.100537342,4_116:0.003566295,(1_2075:0.006659471,0_111:0.016738024)0.596:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000260_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000260_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc300a39485a4d73b81fb04c6aaf6f597fdf9df1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000260_tree_id.txt
@@ -0,0 +1 @@
+(2_250:0.052983753,3_184:0.109608269,(0_117:0.055876206,(1_2082:0.019722417,4_125:0.003796510)0.999:0.058251629)0.530:0.026898576);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000263_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000263_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed1f0eb5c3f8011d7542510bddcfdb7f31e9c8b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000263_tree_id.txt
@@ -0,0 +1 @@
+(1_2085:0.006473292,4_128:0.003186677,(0_120:0.023279713,(2_247:0.115011632,3_181:0.046671116)1.000:0.484680624)0.878:0.026971929);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000271_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000271_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7a7640f43290f8078fd7b2fec3eda178a1476b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000271_tree_id.txt
@@ -0,0 +1 @@
+(1_2095:0.003289904,4_138:0.006546953,(0_130:0.000000006,(2_236:0.145802620,3_170:0.123180814)1.000:0.108091540)0.285:0.009807889);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000272_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000272_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39ad001f75e7b87d82140644c77a593fc9c050b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000272_tree_id.txt
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+(3_169:0.382279353,2_235:0.016352545,(1_2096:0.016395914,(0_131:0.0,4_139:0.0):0.006575175)0.472:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000273_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000273_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8af475dfba64167ab239385d548a5cb321b0d939
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000273_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000278_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000278_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..17c47bd2891824cadb89b67aaf7e4fa543a08ce9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000278_tree_id.txt
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+(4_146:0.008738071,1_2103:0.000000005,(0_138:0.008866711,(2_228:0.029048357,3_163:0.038030412)0.996:0.044057397)0.639:0.002734959);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000279_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000279_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5743f587916f19e55f5d7bbe1fb941ff1223096a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000279_tree_id.txt
@@ -0,0 +1 @@
+(0_139:0.002002060,(1_2104:0.0,4_147:0.0):0.000000005,(2_226:0.048215741,3_803:0.519093450)0.908:0.025656854);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000282_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000282_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..51b5aa40d92e372bc9094c6d28b7303a49b8d348
--- /dev/null
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@@ -0,0 +1 @@
+(0_142:0.000000005,1_2107:0.000000005,(4_150:0.002372677,(2_223:0.086043972,3_162:0.417961975)0.977:0.062993663)0.913:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000283_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000283_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f31dca1cfb0515f40ca11bd3d98fc84c91c3a3ef
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000283_tree_id.txt
@@ -0,0 +1 @@
+(4_151:0.006971012,1_2108:0.006962756,(0_143:0.000000005,(2_222:0.052447023,3_161:0.092682571)0.879:0.032946409)0.833:0.006976555);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000287_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000287_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..07aaffad4ecc816f68e28c2847eb0e21c567122f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000287_tree_id.txt
@@ -0,0 +1 @@
+(0_170:0.006013233,4_167:0.051023507,(1_2117:0.025195079,(2_213:0.014930414,3_159:1.301935444)0.756:0.042815500)0.314:0.014495701);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000289_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000289_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..56b6780c33a41d557c5cb8accc246384d660f164
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000289_tree_id.txt
@@ -0,0 +1 @@
+((2_211:0.020246393,3_156:0.105614088)0.991:0.017195929,1_2119:0.002695845,(4_169:0.005400895,0_172:0.002690686)0.759:0.001322414);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000291_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000291_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03e10dead3c3058497357e6c908eca5792d72e1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000291_tree_id.txt
@@ -0,0 +1 @@
+(0_174:0.026551310,(1_2121:0.0,4_171:0.0):0.026995738,(2_209:0.013866248,3_154:0.671995932)0.932:0.044445497);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000293_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000293_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa865ffd90d66472d12528c6c036cb9d98b587f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000293_tree_id.txt
@@ -0,0 +1 @@
+(2_207:0.023636339,1_2123:0.003588093,(0_176:0.001955603,(3_152:0.038477929,4_173:0.007795632)0.937:0.010355639)0.667:0.003453639);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000294_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000294_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5eb5bd54407be5798002e29073aa749c3ebfb3b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000294_tree_id.txt
@@ -0,0 +1 @@
+(2_206:0.015239860,3_151:0.134285436,(0_177:0.002245170,(1_2124:0.019605555,4_174:0.000000005)0.857:0.021958110)0.664:0.015547684);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000296_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000296_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff433d2f853c75da104152f6f93292ecd0505e28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000296_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000298_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000298_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20b8944168a712fdea4bbf5c6c89b22589279939
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000298_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000299_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000299_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..51ea61e45f79fc225225e8bc0fe761b98e453513
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000299_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000300_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000300_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c90e67139488741e63e8d5644a22088e5d362ee9
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000300_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000302_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000302_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..80fed8ef2d61407149fcd657467b67c1c8d3111a
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+(0_189:0.029096377,1_2136:0.019231834,(4_189:0.047171829,(2_192:0.249471778,3_140:0.266721108)1.000:0.249170630)0.736:0.010902472);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000308_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000308_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c82966bf79c6652f4db146e2b822e7d1a41bd32d
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000311_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000311_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bf091efb41cc57d9bf3535d99e28ec8c98f799f2
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000312_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000312_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34acf97314834f3fee3df07afc8722933567f758
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@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000313_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000313_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a2a7525655d617ed9dfcf88f3811c5a458bedcba
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000314_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000314_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9160fd6d03c38fd3671b29eb79c88e31b206bd1b
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000314_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000316_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000316_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed953b9e18950431303cfa129cbf5b34f92f63b6
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000319_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000319_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e4a6d7ed149846e36abb898df5213eaf5c2d7ac
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+(0_218:0.010947462,4_219:0.011072580,(1_2182:0.010451420,(2_144:0.179400432,3_102:0.284609105)1.000:0.143731866)0.538:0.006843160);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000320_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000320_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2969bdf910fdee71e647c89692f4d7eb0162c5d4
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000329_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000329_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d790407f30e88f8fc9f0cbcb5a7e9ece75836761
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000330_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000330_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b9afcc98d776b91b6ac4fda7dd96963f9673eede
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000331_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000331_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e58b2a227c3288387dc8c536a6220eff55ea4d8
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000334_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000334_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4d79f1bab2c5a82bb849941551dd8aaffa64c0c
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000337_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000337_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65a794ef24a1e0d5125a07af514fe6534f3eaa31
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000339_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000339_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a91ba23abae6eb0a05a14c549a95d8dabdd4abbf
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000340_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000340_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..71b3efef7ac91f81df1d39fb6bc8dec0ed609931
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000342_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000342_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f946490cfa76c524d164c854cb7db036cde9ff2
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000344_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000344_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b92e7b299f437d1bcb819aef56180101edf31f53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000344_tree_id.txt
@@ -0,0 +1 @@
+((0_256:0.0,1_2220:0.0,4_254:0.0):0.009474027,2_89:0.078102178,3_60:0.116002560);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000345_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000345_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68a8bc75580bd0394549f255e9f6f068474f33b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000345_tree_id.txt
@@ -0,0 +1 @@
+(0_257:0.023853203,4_255:0.009438963,(1_2221:0.004759194,(2_88:0.053806745,3_59:0.107566678)0.997:0.077187992)0.750:0.004734000);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000346_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000346_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..117a40d1895b98166ccc89a6846699128b003a2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000346_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000347_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000347_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0acac3c257a92834bea40bf922760cd2f63d1b8f
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000347_tree_id.txt
@@ -0,0 +1 @@
+(0_259:0.002419953,(1_2223:0.0,4_257:0.0):0.002472297,(2_86:0.020443333,3_57:0.328242687)0.968:0.030600552);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000350_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000350_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2aa232a01d5fbd8e5ca7158508c617adde87a3fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000350_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000351_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000351_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44830ba2e3c37249b8a49c1fdd96c638ae2e5325
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000351_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000352_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000352_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..08a720d8ce92d256517d0a44f2a7087fc5a6e52c
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000352_tree_id.txt
@@ -0,0 +1 @@
+((0_269:0.0,1_2235:0.0,4_268:0.0):0.000000005,2_66:0.005710089,3_51:0.111836669);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000353_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000353_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fbc69cf29260ffe39b0e231ed6517381b32e54bf
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000353_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000354_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000354_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0077b524163f4937ff6f1ceecb39a6ee255cf82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000354_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000357_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000357_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78e9b33cb4ce98a5ba2e7c841bd4de520c0849ba
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000357_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000359_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000359_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2586817b534a90071eba8cee28fb0cbe91a86a85
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000362_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000362_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30f31c0523a69b5ad16e28f3d6d393dfa3f34f50
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000363_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000363_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b95a87f4a520c403df0e914c877873caee273f62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000363_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000364_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000364_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ec1a0162e18547a4ae47293ad74ab938b2c81f4
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000366_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000366_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3a5d809bde059fa89db42c6ea21385d75b65aa8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000366_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000368_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000368_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e43b6b66b2cfd07d36f678786530140bab600448
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000368_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000370_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000370_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f8129ae3992f39f73603434c320a917cfabc47e
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000370_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000373_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000373_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7f9c796b09d3e515602d6d0f6ae06dd643f5beb
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000378_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000378_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b4aeadebaebf03780c37f867a47ec9f590084a3
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+(1_27:0.007271738,4_310:0.000000005,(0_303:0.021910077,(2_16:0.054109097,3_12:0.284254936)0.984:0.059520103)0.925:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000379_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000379_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84b6308794467ef18a54b5643c6d114f4a334012
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000382_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000382_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..453adf42b599aa3673abe6a98dc052b47db4b7ab
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000383_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000383_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f755a86d30a48625714da4084241e0d4d26835e
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000387_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000387_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c558855e10f63645395ee94011ff0af3c02563b1
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000387_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000389_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000389_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..404362d603543eee5a0542573589e6da79669d3f
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000390_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000390_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a43d3c3e2c61c816962b3021488653354090fb03
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000390_tree_id.txt
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+(1_44:0.015563724,4_326:0.025910761,(0_319:0.045357299,(2_2617:0.232839025,3_2428:0.139450855)0.996:0.162581455)0.854:0.022919591);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000391_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000391_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ceddfc4d9b4950c54c3665fe15552d51e7c8eb8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000391_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000392_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000392_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e762e0721193914e7bb4578a7b546c9da1dd7f82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000392_tree_id.txt
@@ -0,0 +1 @@
+(1_46:0.019153065,4_328:0.007169219,(0_321:0.009918759,(2_2614:0.194300765,3_2425:0.593695880)0.999:0.161804071)0.783:0.017501216);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000393_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000393_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e704cf6f2869a1e891853f6e716de449d3ea69b
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000393_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000396_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000396_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0528974bf1cd1e31ae2ceaf4ea60570990ea17c
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000396_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000397_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000397_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..878c30d43caef13fe639ce4a31b53896907ea3c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000397_tree_id.txt
@@ -0,0 +1 @@
+(4_333:0.018289731,1_51:0.008370791,(0_326:0.003329071,(2_2566:0.076853826,3_2417:0.297874398)0.999:0.071849522)0.468:0.004338586);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000399_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000399_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..82f6d2231b18657ef7631bbd8a1581c06092e70b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000399_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000402_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000402_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cdfb8e908d2dec5a68765a13620d28488b11b19e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000402_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000406_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000406_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4489dacbc657cb5ad07abe312945519e22c29256
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000406_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000410_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000410_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4244968080122ba4e6cf79d0e6c39c22fc8af86
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000412_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000412_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84c16dc6189185ae89545198d9b4d350944f73e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000412_tree_id.txt
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+(0_344:0.012353682,4_351:0.007481546,(1_69:0.003866334,(2_2540:0.097869637,3_2399:0.244848912)0.884:0.047052784)0.466:0.005581372);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000417_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000417_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..686098853bcb4db53c92eb43799d9a35a82385d3
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000419_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000419_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae0e1cf0019ba619318bb2cd0fa9935379975249
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000422_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000422_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ee964f6833a3c5bd291eeb52eeada4119e437e2
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000424_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000424_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d60f337d68e302c631d00a1486beeba5ea39467
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000428_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000428_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..76aabf89f8f2c15c732451301de8cd0591114380
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000429_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000429_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c2ed57087ecd2eee8e2dacb42cccb8da2599c98
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000430_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000430_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b194dac3ee372f4ab5b202ac79b486e0319d7108
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000431_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000431_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..680693f3d08069ea14672198cf64b937a9ed1f5b
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000432_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000432_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..309f74054b08e689fac504191a56b4a1db80a0bd
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000434_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000434_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..037edf4e7ee6ec58131320b0e3dd913a8759c72f
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000437_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000437_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d1d5fe042cb342ec8b7b9d15209cf30a2caf25c
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000439_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000439_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d00b8f231f4e2152ca8a8df888c94e1650359ca1
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000440_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000440_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05d0a6e48b423f60050cd4e11f291e4714592faf
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000443_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000443_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7638edaa9dd310b62dac82451d146502442bba6d
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000445_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000445_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7276642e404303fee1d29886ef6079abe1135280
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000445_tree_id.txt
@@ -0,0 +1 @@
+(2_2492:0.009366681,3_2360:0.009959981,((0_390:0.0,1_119:0.0):0.002459602,4_393:0.009923887)0.981:0.015217583);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000446_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000446_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a800862ead2a770da4def113cf83c92b5c062870
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000446_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000447_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000447_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63d173a433269246d7fa4cab3d037069cc51a753
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000447_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000448_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000448_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27a7db74ac0b004c86d8683e6b385ba7d6fdc763
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000448_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000453_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000453_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b2d974c1a2712b9e831e825377c90b4b3756c91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000453_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000455_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000455_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b46634e2d4d2b0287b4834f64c68acd8ec487701
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000455_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000457_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000457_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..79a77fcbbe53b7bb5df045c7cd9b09d36c0d2bfd
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000457_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000460_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000460_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..256da88754ba4b878d8e2a7e01a0826fde9db79a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000460_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000461_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000461_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9da56fea8ed1f1944cd30682e4c5bb9c6594fb3e
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000461_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000462_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000462_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7bf5a20610d1a590085c4d12e523a9d4631db09
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000464_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000464_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3a622f460466536fe6be27bcac6756bdc1e30fe6
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000465_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000465_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8986ecc590e295c12ac8f9847194cbd6ae113887
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000466_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000466_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28f6217588e00027e6120c0a42af5df8ab307b39
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000471_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000471_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..04ff6ead8a9bcf04d0df46e7f08cd2a32060399a
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000472_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000472_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8bd7ac6ba80adf41a3e44edddd7e1dfc8e5683f
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000473_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000473_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f29bac310b17cc843f3ea2386854f2aa33f4655
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000474_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000474_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ee3e44ccfa6daecc092787b5f88fea50051178c
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000475_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000475_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5fb51934009be6ff3f774710f2d61d46126e10b2
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000476_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000476_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad1f71f7818332b26140fb900002fb37a8d36567
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000479_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000479_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3b73b45f9550fcf2abe4814c0d4d428efd99f22
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000481_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000481_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc4580a0e6665bfa60acfc8664894354a6cf2b29
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000482_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000482_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..549814ecb12e3d39d3dbdb976f794a2963fe0a99
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000484_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000484_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ffad5d0de29edc38f6721e37245e6f5845bddd8c
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000487_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000487_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d25b64ce91534adf6d9b610cd0dcb574902891a7
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000488_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000488_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..348de2a94d6cfc2d77e9db2a885c6b80b7b92dbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000488_tree_id.txt
@@ -0,0 +1 @@
+(0_443:0.000000005,1_170:0.004272588,(4_443:0.000000005,(2_2428:0.046594250,3_2311:0.229780039)0.986:0.057065799)0.894:0.008588277);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000492_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000492_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..019529fa99c50c347b0501823b00d54f5f318542
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000492_tree_id.txt
@@ -0,0 +1 @@
+(2_2424:0.191295068,3_2307:0.416951377,(0_447:0.014169693,(1_174:0.0,4_447:0.0):0.024555543)0.948:0.106562467);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000497_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000497_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfb506e50071c593efd04588426af074352679b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000497_tree_id.txt
@@ -0,0 +1 @@
+(0_452:0.002386702,4_452:0.000000005,(1_179:0.009720377,(2_2419:0.091902890,3_2302:0.449743366)0.951:0.048527350)0.762:0.004771027);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000503_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000503_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63231809560d0ae51505e8bc1c865e28353304f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000503_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000504_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000504_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c039df0be158349d5b358f9c263b9487541ccd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000504_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000507_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000507_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fdfd18835a794e13bf73f0f9eb68f47039513313
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000507_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000510_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000510_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b09476abe84ea7f65514828ddeeaa55f8a4c3f2
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000510_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000511_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000511_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ec4beb9c03826977c8a647096f7c90036ebf0ed
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000511_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000520_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000520_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..976dcd95ab328eedd49b867cd83de8390c0c1c2a
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000521_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000521_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5a326496ba1bad13328d430b8db0c6f6af124f72
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000525_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000525_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..972813dc31e4ad64786ec7bc99b4202e3f7dde2a
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000526_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000526_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e3b4f118ca9062b1a71bda6e8eb079ef2b38568c
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+(4_489:0.075343379,(0_490:0.082488685,1_219:0.062053227)0.998:0.083227314,(2_2385:0.069248873,3_2267:0.146720506)0.667:0.048433942);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000527_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000527_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc0ae7c47551b22c0be568984f316e536a28f836
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000532_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000532_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9bad9311fb502c870e33a2cf814381a8329d485d
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000536_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000536_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44823c573f352569cdedf824ac3e9e1181903c98
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000538_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000538_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c78f12e82954d1baa053d7f4d1d910529a14bc70
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000539_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000539_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c71a9c99d212b49aab8a15d31134839fb78e451
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000541_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000541_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9d1c9caff4c9779617b7f89b94d2359614a23c4
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000542_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000542_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8112c4791d716c607fc642f917ccae2e7b0f8707
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000545_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000545_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f93bdaa7d79db73896ff5164c112a172d5586b7a
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000547_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000547_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5919da05dc587d550b3897052545e602951e7e72
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000548_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000548_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..459f1397315037c2a372cd822acaddf073c16583
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000549_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000549_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5a2cd00a48258a38c46025df310de07e1b70f68
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000550_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000550_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..440d67c68c1b3d69bcdab8ece4e0618f97e4e060
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+(2_2341:0.040450739,3_2225:0.150488479,((0_528:0.0,1_262:0.0):0.003250232,4_531:0.000000005)1.000:0.101668087);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000551_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000551_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c474aa9b16793592ad83f007c6a34f52dcba473
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000551_tree_id.txt
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+(2_2340:0.128946994,3_2224:0.174555008,((0_529:0.0,1_263:0.0):0.000000005,4_532:0.032360826)1.000:0.673542184);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000552_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000552_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3643a0bc62a1bbd1877ff04e51db67f7ca42343
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000552_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000553_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000553_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dbc527d158037110a68380539c716a68f52316cb
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000553_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000554_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000554_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5ecb590a2105deedf4dea3bc69e30a191034cfd
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000554_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000555_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000555_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..047a99dbe06014f9e635e0ed56ef8ef7f38209b4
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000556_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000556_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..72ade9f786b403db7df245c37ba0e7363a048a58
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000557_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000557_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b88be701724eeaaba9e37ac6d162f15294b052f5
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000559_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000559_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74efba1a150f0bca92e54f17cbd2acf56a367b08
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000560_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000560_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..715536bdc73e5cc63ea0dc1dbf21343e1cb5602d
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000564_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000564_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a006fdf6e9668d076b525f1c5523bc6f720eaf77
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000567_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000567_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c20d885622e9b67667bbafd984ded5fff8d4764
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000571_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000571_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fad7c89202611a54d3d0811a57f59a6ea15a5a0a
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000573_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000573_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..329148e1e488a25409fb94045512eac8e29d413d
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000574_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000574_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9082dd334ef8f9323e869ff6d309037a8fbfbba5
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000576_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000576_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b87f92eaa365a86323f6d48f629698a4de152902
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000585_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000585_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7566f27c3ded79be5c28ebc577f036bcbf05bdd
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000587_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000587_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..07a3898ce532c86ac2c34c62cc3fa3d4a2381303
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000591_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000591_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0eb92dd7cd01fdb75ea79336ef81bbf8821ce44
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000595_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000595_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4a8824c084e582a26c23d36c6247dde18ea50f6
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000599_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000599_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..389bb3efd68c55d9aab1271d76f8915788362ea6
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new file mode 100644
index 0000000000000000000000000000000000000000..a6cb4d7b555a3e0761e0f2e858294a475c0f090e
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000604_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000604_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d95b480bbcbd68543261d1cb4c852138b6906704
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000605_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000605_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5d4e3667badeadc9ae9ca3eacaf26a716e773d9
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000607_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000607_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d190e3a0ac6ee8d352596926e99b622adec6f317
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000612_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000612_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3046dcea820dce8c415bab313d7e465731538e84
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000616_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000616_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63f9c51a9241bda7d31678630d4348614bff9a6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000616_tree_id.txt
@@ -0,0 +1 @@
+((0_663:0.0,1_409:0.0):0.002229442,4_633:0.000000005,(2_2216:0.029163750,3_2084:0.112710931)0.984:0.032045818);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000618_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000618_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f92aafa392a76fc627c887c471fa7d0b2c05269
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000618_tree_id.txt
@@ -0,0 +1 @@
+((2_2214:0.046601765,3_2081:0.543246026)0.985:0.154239864,4_635:0.000000006,(0_665:0.035784697,1_411:0.000000006)0.845:0.005772684);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000623_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000623_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e9375c1b4faeeb4d0dcb354875131ad5cbc5e17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000623_tree_id.txt
@@ -0,0 +1 @@
+((2_2207:0.084912694,3_2077:0.387131030)0.998:0.175662434,4_641:0.009656254,(0_671:0.041491943,1_417:0.005651525)0.699:0.007796131);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000624_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000624_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c852c1cb5e7c5d3b35e1d95418510f4840f52fbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000624_tree_id.txt
@@ -0,0 +1 @@
+((0_673:0.0,1_419:0.0,4_643:0.0):0.013868900,2_2205:0.051323950,3_2076:0.219480767);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000625_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000625_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..027c526a0e0bd8d37e770799bedde1f0b92cfc02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000625_tree_id.txt
@@ -0,0 +1 @@
+((0_674:0.0,1_420:0.0,4_644:0.0):0.024973628,2_2204:0.063794204,3_2075:0.222274376);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000626_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000626_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bdbb8599bf9cccb793216976415caecc253a6527
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000626_tree_id.txt
@@ -0,0 +1 @@
+(2_2203:0.015901167,3_2074:0.054059913,((0_678:0.0,1_421:0.0):0.000000005,4_645:0.002766068)0.874:0.007549369);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000627_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000627_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1013f93db5de88d6c27c330fcf44076530957d61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000627_tree_id.txt
@@ -0,0 +1 @@
+(1_422:0.010609016,4_646:0.007171054,(0_679:0.029078457,(2_2202:0.104551193,3_2073:0.222372282)0.987:0.214121900)0.949:0.030739547);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000628_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000628_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a3255927f78796470ffe7cd8c5c49a9710b624f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000628_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000629_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000629_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb6197f26f0567e98716dc26e98af116ff42b0bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000629_tree_id.txt
@@ -0,0 +1 @@
+(1_424:0.016051095,4_648:0.011332148,(0_681:0.023414279,(2_2200:0.217798885,3_2071:0.010667996)0.805:0.011362453)0.847:0.011213893);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000631_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000631_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e52d1f2e69a82360679658508304e1a36ed95dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000631_tree_id.txt
@@ -0,0 +1 @@
+(0_683:0.008864244,(2_2196:0.013891513,3_2068:0.024107351)1.000:0.302987714,(1_426:0.000000005,4_650:0.004721219)0.866:0.015085640);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000633_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000633_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67f0a7ad1fefb871a56c200ca2310b26f3710bcd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000633_tree_id.txt
@@ -0,0 +1 @@
+(0_688:0.008843168,4_652:0.000000005,(1_428:0.005359877,(2_2194:0.047434089,3_2065:0.073167477)0.999:0.038757229)0.544:0.003488721);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000635_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000635_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..134388153232ffd982dbdf5ee382a4614bd6bba1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000635_tree_id.txt
@@ -0,0 +1 @@
+(0_690:0.004092813,4_654:0.008167286,(1_430:0.004027545,(2_2192:0.014296422,3_2063:0.150722849)0.989:0.053312067)0.410:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000636_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000636_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd770a80d0e96ef1ca167c3359a390a5754124d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000636_tree_id.txt
@@ -0,0 +1 @@
+((0_691:0.0,1_431:0.0,4_655:0.0):0.063134451,2_2191:0.064831248,3_2062:0.435291003);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000637_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000637_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df2bca0e61858e17a7c505aafe6abc7d90936703
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000637_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000639_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000639_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a800ea82b6cb7826a76fac96dafbe250d096e15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000639_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000645_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000645_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3dce92c56863adceb03029a77f74ec38975625bf
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000645_tree_id.txt
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+((0_700:0.0,1_440:0.0,4_664:0.0):0.119692886,2_2182:0.062138914,3_2053:0.317628445);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000648_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000648_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..afab933f4753ee8f920cd0bf1b07867a17f29d9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000648_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000650_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000650_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ecd03110fdc64e75c4c21a27286a6a0cd522443
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000650_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000652_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000652_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3431f474fe83b75c43819b9b9d86dbc2a3b8149e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000652_tree_id.txt
@@ -0,0 +1 @@
+(0_708:0.003167943,1_448:0.000000005,(4_672:0.008837489,(2_2169:0.097870207,3_2044:0.322234226)0.995:0.106742616)0.830:0.010609888);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000653_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000653_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d45b39a67e337191d7b0ab84f577cc9a4368a8d9
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000653_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000654_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000654_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f87b16626659749f6acc9ac6c56199c86fd9b114
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000654_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000655_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000655_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81e4b69dc8304afcb654a5482fa6738fb89f7c91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000655_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000656_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000656_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..79edbcf1b860509f7f4030194671028d59f4e20f
--- /dev/null
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@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000658_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000658_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45b99645181fbe0f3a3e945eae7c7b71556fe192
--- /dev/null
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@@ -0,0 +1 @@
+(3_2035:0.005613974,1_455:0.002797372,((2_2138:0.014097495,4_680:0.000000005)0.865:0.002798541,0_715:0.002798655)0.324:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000659_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000659_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd98c31dfe14e7cb80e27958970d1946c6e62492
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000659_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000660_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000660_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31d85b281be52f4d138bc989656a6510d2bd8d3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000660_tree_id.txt
@@ -0,0 +1 @@
+(1_457:0.007473749,4_682:0.000000005,(3_2033:0.018955124,(2_2136:0.067309012,0_717:0.007533878)0.303:0.000000005)0.775:0.003701404);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000664_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000664_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90c4c9c85a3e7dbb84a6e6a59bf5005759ededd7
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000664_tree_id.txt
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+(0_724:0.007893322,1_463:0.005354323,(4_688:0.002495260,(2_2130:0.045401753,3_2024:0.158294854)0.863:0.014316568)0.350:0.002956868);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000665_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000665_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fc607e0767f7144804199c0337ebb849db97473
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000665_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000667_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000667_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f6eb753752d046cb90bdda9c61a0ceae50e1c26
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000668_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000668_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..415e14cf7498e5aa71708ca77cb456f0a4adc6b6
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000669_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000669_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4754b51aa7fd40746d2dd5b1e091b47ecd87fc3a
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000672_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000672_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c97cdd785d191b90f4a716097158c3921d7ef12
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000674_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000674_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9aef8d58e1de1235bc08cbd4e9cc1f755f731395
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000677_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000677_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bbff5325c9131dd2a2e6c02e12eddee66fcc9da8
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000679_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000679_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5fa78887fadd1de32921cce5163f75f332882a9
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000680_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000680_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02345163e1d1f2393e9364d979efd3cdd1b6e8b9
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000681_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000681_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5fbc1b9cf1ddf73d3a12d8c5b7695e7813b35ea1
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000682_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000682_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98be7a9260142880e2af35ddedffdb896b553bc3
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000683_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000683_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5369daaf854bdc95f8487f271f4881a1c249814a
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000686_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000686_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bdcf78f8693a72088e3d73800b5437fc602e5084
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000687_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000687_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..635543fac57002a03f81a6e0bda198a7c113ab79
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000691_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000691_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e9f9e2c25d84d8140e5d80a2cfebfcd4c03fc15c
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000697_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000697_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..07df0c62e08d1db2eb8d46cbcf69cafa3b21a85f
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000701_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000701_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8cf761b6981a1078a1bb1843e15e686f43a5bbc1
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000705_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000705_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86368572e918d4341a34598ef1f00b1083e2c28f
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000710_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000710_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7eb756e17bc5e6e73de301c2a3036d0d873efeeb
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000712_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000712_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..696df93490395270a906c84e4b5fb860743bb4c8
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000713_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000713_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d3e322478697aefe55f24ce533cbda871b84bb4
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000718_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000718_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..baafae4b956a83ae1140a48ad25a920de1428bbf
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000720_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000720_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc06d8edb8f496f134115b8a13387242bc959b87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000720_tree_id.txt
@@ -0,0 +1 @@
+(2_2069:0.048651063,3_1959:0.132056438,(0_785:0.005134419,(1_526:0.0,4_754:0.0):0.010677252)1.000:0.127320052);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000722_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000722_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa221013be68196fd32eb3005327c947a16c1e26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000722_tree_id.txt
@@ -0,0 +1 @@
+(2_2067:0.023195420,3_1957:0.121366748,((0_787:0.0,4_756:0.0):0.000000005,1_528:0.003805450)0.962:0.037691658);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000723_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000723_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5236de26b0813acba26bee3af0d02f442c41b95a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000723_tree_id.txt
@@ -0,0 +1 @@
+(1_529:0.000000005,4_757:0.004308982,(0_788:0.005438869,(2_2066:0.096261158,3_1956:0.167538397)0.697:0.024734293)0.632:0.003192777);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000725_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000725_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc4196d6a5788b59947e57c8deba4f7304d51522
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000725_tree_id.txt
@@ -0,0 +1 @@
+((2_2064:0.168727538,3_1954:0.284109274)1.000:0.197159157,1_531:0.000000005,(4_759:0.015798613,0_790:0.000000005)0.810:0.005173283);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000727_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000727_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c7fdeb168b60dba44223033166ed9506767f9e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000727_tree_id.txt
@@ -0,0 +1 @@
+(0_792:0.000922964,4_761:0.002839514,(1_533:0.010871873,(2_2062:0.224277011,3_1952:0.259323789)1.000:0.349840884)0.483:0.006228114);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000728_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000728_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de90f244ca194c2b9f02f3100f76a828bdbb7b75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000728_tree_id.txt
@@ -0,0 +1 @@
+(1_534:0.000000005,4_762:0.001796715,(0_793:0.008850852,(2_2061:0.066744024,3_1951:0.221342692)1.000:0.082005453)0.834:0.002932673);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000729_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000729_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..532a2100e4a313601b6a3dbd15bd106593078db7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000729_tree_id.txt
@@ -0,0 +1 @@
+(2_2060:0.056137167,3_1950:0.133790011,((0_794:0.0,1_535:0.0):0.000788166,4_763:0.007354898)1.000:0.074936864);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000730_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000730_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88cc8d9540ee0cdeb55ebe3be54e0809b1f3c70e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000730_tree_id.txt
@@ -0,0 +1 @@
+((0_795:0.0,1_536:0.0):0.011698775,4_764:0.010331666,(2_2059:0.123931147,3_1949:0.384970262)0.999:0.119428867);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000733_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000733_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e23d49aa4de31b46beef06de66fe167c60bdda7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000733_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000736_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000736_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc25e1fe9c5ed315cde14c7df8bad5a6a09a4876
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000736_tree_id.txt
@@ -0,0 +1 @@
+((0_802:0.0,1_543:0.0,2_2046:0.0):0.000000005,3_1944:0.084364467,4_772:0.005682460);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000737_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000737_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10efd27ed049f6c84eebe27e3b69137b9c337547
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000737_tree_id.txt
@@ -0,0 +1 @@
+(3_1943:0.069947107,4_773:0.002888302,(1_544:0.000000005,(0_803:0.002892649,2_2045:0.005785973)0.750:0.002893780)0.113:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000738_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000738_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bce6408ddc31115e435f607b027c852f4409b1d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000738_tree_id.txt
@@ -0,0 +1 @@
+(2_2044:0.033046234,3_1942:0.189863269,(0_804:0.007193940,(1_545:0.0,4_774:0.0):0.000000005)0.986:0.030074136);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000739_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000739_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d950a66f34c099c4ead62c4285770a092fba2c27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000739_tree_id.txt
@@ -0,0 +1 @@
+((0_817:0.0,4_776:0.0):0.000000005,1_548:0.001850255,(2_2042:0.037866289,3_1941:0.163031124)1.000:0.058921821);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000741_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000741_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53d53e6967c84cb4181f37ba8a227f4cb87e0563
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000741_tree_id.txt
@@ -0,0 +1 @@
+(2_2040:0.069558239,3_1939:0.032979043,(0_819:0.007040108,(1_550:0.0,4_778:0.0):0.004147257)0.920:0.013980114);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000743_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000743_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2cac4adb1dfe9afb027f373798831528982bc77e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000743_tree_id.txt
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+(0_821:0.096825727,(1_552:0.0,4_780:0.0):0.091470915,(2_2038:0.151806585,3_1937:0.112343802)0.914:0.133003336);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000745_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000745_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1ec9230ebcc484e7de1c29d7f8516e525ea6bb4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000745_tree_id.txt
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+(0_823:0.004110160,(1_554:0.0,4_782:0.0):0.011309571,(2_2035:0.039518292,3_1929:0.099703290)0.992:0.036049862);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000746_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000746_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa1566c41f9a160df91c7428983d0b37d1e9c3b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000746_tree_id.txt
@@ -0,0 +1 @@
+(1_557:0.008794252,4_785:0.006823690,(0_826:0.005079983,(2_2033:0.054964803,3_1926:0.172003934)0.995:0.047118825)0.623:0.001756502);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000748_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000748_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a092475a36fb1415270dafa451c3642d8adf83e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000748_tree_id.txt
@@ -0,0 +1 @@
+(0_828:0.002007211,1_559:0.000000005,(4_787:0.002700129,(2_2031:0.085566672,3_1924:0.122139212)0.982:0.039489900)0.900:0.007367413);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000749_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000749_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41a4d769edef532248cbbfef1bc5bc6a4768c830
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000749_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000750_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000750_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0574d77e91e6f59203903ff525c0c1575e8efc7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000750_tree_id.txt
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+(2_2029:0.016283295,3_1922:0.066819761,((0_830:0.0,4_789:0.0):0.007537201,1_561:0.002746952)0.993:0.026680639);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000751_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000751_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7fee96c6ec8fac942d937ec38a615f827f38d47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000751_tree_id.txt
@@ -0,0 +1 @@
+(2_2028:0.009508199,3_1921:0.168900031,((0_831:0.0,4_790:0.0):0.004942572,1_562:0.004922763)0.941:0.031124998);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000753_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000753_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2cac04221c6304138f19add9f46d94b7bd5b49e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000753_tree_id.txt
@@ -0,0 +1 @@
+(0_833:0.019794069,4_792:0.007734848,(1_564:0.000000005,(2_2026:0.072648389,3_1919:0.244716298)1.000:0.135808434)0.760:0.004173792);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000754_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000754_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c6fb868e4d5ded9e1ffd2ca7237f78e3d0d6e4bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000754_tree_id.txt
@@ -0,0 +1 @@
+((2_2025:0.043217919,3_1918:0.182680177)0.986:0.040497327,4_793:0.002710258,(1_565:0.005421841,0_834:0.005445494)0.438:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000755_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000755_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2efd1db0311d3d16f0a00696235af74de0248bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000755_tree_id.txt
@@ -0,0 +1 @@
+(0_835:0.000000005,1_566:0.005344898,(4_794:0.006269955,(2_2024:0.050297970,3_1917:0.171322777)0.979:0.050658847)0.775:0.004500783);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000756_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000756_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ab84f052bbe53c203cf45ce1ad75fc3a570e542
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000756_tree_id.txt
@@ -0,0 +1 @@
+(0_836:0.006050516,1_567:0.000000005,(4_795:0.000000005,(2_2023:0.081438019,3_1916:0.319747118)0.847:0.032507529)0.914:0.012024655);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000757_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000757_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c4c28c434e228160f42a79598d4e223db041d5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000757_tree_id.txt
@@ -0,0 +1 @@
+(2_2022:0.011541682,(0_837:0.002579807,4_796:0.002588213)0.873:0.005135199,(1_568:0.002589794,3_1915:0.464683370)0.803:0.005259597);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000758_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000758_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dab21018f3c8fa5ff67bde3d5ece769fa1a1411e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000758_tree_id.txt
@@ -0,0 +1 @@
+(4_797:0.004864929,(2_2021:0.112795923,3_1914:0.506927806)0.954:0.065148684,(1_569:0.008646620,0_838:0.018486642)0.811:0.006644069);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000761_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000761_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27930865dfb4fe8bdce6292223618484d2bf1a6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000761_tree_id.txt
@@ -0,0 +1 @@
+(0_841:0.009154186,4_800:0.009918855,(1_572:0.011678228,(2_2018:0.037043212,3_1911:0.307564247)0.910:0.029288740)0.896:0.012691426);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000763_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000763_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8ccd9c3e6d908a781f7857a0e7e8cdb39b0c6c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000763_tree_id.txt
@@ -0,0 +1 @@
+(0_843:0.003295635,4_802:0.003301336,(1_574:0.003190036,(2_2016:0.028517275,3_1909:0.163756969)0.991:0.059703503)0.318:0.003423392);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000765_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000765_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd0f4bd3a963de2bd0aa5b2077967e47626dff51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000765_tree_id.txt
@@ -0,0 +1 @@
+((0_845:0.0,1_576:0.0,4_804:0.0):0.013313063,2_2014:0.000695741,3_1907:0.060777650);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000766_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000766_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..733b6abc6f99a380c6aded190663ee5229e25dac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000766_tree_id.txt
@@ -0,0 +1 @@
+(2_2013:0.042225657,3_1906:0.137837346,(0_846:0.000000005,(1_577:0.0,4_805:0.0):0.004477454)0.722:0.003399793);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000768_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000768_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ddeae623ee3b25b8070fa7ca7f1a0a17f1c767b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000768_tree_id.txt
@@ -0,0 +1 @@
+(0_848:0.018756726,4_807:0.013241279,(1_579:0.002836504,(2_2011:0.117469971,3_1904:0.563561060)0.997:0.137558352)0.773:0.005233083);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000772_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000772_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50e02561e660c3a3ded47e07507c3c0e0dd8e351
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000772_tree_id.txt
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+(0_863:0.000000005,1_594:0.013662830,(2_2000:0.253540668,(3_1897:0.486334347,4_814:0.736991501)0.997:0.370771914)0.965:0.130065679);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000773_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000773_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e3330b2c67bce3e6e5b0a2fe97b6e80cf3016d80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000773_tree_id.txt
@@ -0,0 +1 @@
+(2_2001:0.005668063,(1_595:0.014672091,3_1898:0.317685075)0.380:0.009717234,(0_864:0.003520551,4_815:0.004648780)0.394:0.005843953);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000776_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000776_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03936f52c3f133277af3e656a53a2315685512a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000776_tree_id.txt
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+(1_598:0.010716718,4_818:0.001439162,((0_870:0.0,2_1996:0.0):0.108215737,3_1893:0.125630308)1.000:0.105835879);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000778_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000778_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13badbbff18a33ae0a914057762dac33d534f50c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000778_tree_id.txt
@@ -0,0 +1 @@
+(2_1994:0.102475320,3_1891:0.056037034,(0_872:0.000000005,(1_600:0.0,4_820:0.0):0.000000006)0.882:0.022589083);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000779_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000779_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8184934f79fac53d7e366b2ca975064a71065a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000779_tree_id.txt
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+((0_873:0.0,1_601:0.0,4_821:0.0):0.012289948,2_1993:0.000000005,3_1890:0.090475721);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000780_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000780_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1fa8eeda0115fa725a8b56ca42c89e5e0ca9929e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000780_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000782_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000782_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ced819f108f98928018aaadefacf4e1ff37033c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000782_tree_id.txt
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+(2_1990:0.062150672,4_824:0.008389032,(1_604:0.008403752,(0_876:0.000000005,3_1887:0.070230175)0.239:0.008361775)0.619:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000783_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000783_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68f7b2ff3f0743cc401f9df0721f759fa9f9c529
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000786_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000786_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ac3188a8932a49e64c6b6a445d1e00ba869d6b17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000786_tree_id.txt
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+((0_880:0.0,1_608:0.0,4_828:0.0):0.072242427,2_1986:0.000000005,3_1883:0.157591081);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000787_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000787_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b69b59cbd38c07339c434cb3aa5d0b3db7f93fed
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000788_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000788_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ba8e3c863de36e5ca7b2b4744b72d9c0d8d68c9
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@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000790_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000790_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..979cb2820d658ae373727d990abf168f813a39b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000790_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000791_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000791_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c94b2080179fbc1f312b380a12f996a371181d57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000791_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000796_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000796_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45d1cb1e6c29f56e8bf8f4a96ee699706f565445
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000798_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000798_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1aac1d29be6f32509a09dbb706be202c023a5516
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000800_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000800_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc7f574b92338e4dfe22da3e2a11b8f48f907bdc
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+(0_894:0.029651775,4_842:0.007244707,(1_622:0.019880347,(2_1970:0.068095872,3_1868:0.375930982)0.998:0.143472026)0.885:0.017504656);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000804_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000804_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..221f4e9287615de710f59179d48a363b867371d0
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000804_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000806_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000806_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7f5575cca102ec51bedd96a8530a10c632fb17db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000806_tree_id.txt
@@ -0,0 +1 @@
+(2_1963:0.058547083,3_1859:0.111326629,(0_900:0.005025927,(1_628:0.0,4_849:0.0):0.000000005)0.961:0.040905279);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000807_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000807_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..713cd1d1caa8f6147ecdb3b924a3ac34cd8e4a15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000807_tree_id.txt
@@ -0,0 +1 @@
+(2_1962:0.019797490,3_1858:0.090624771,(0_901:0.003126069,(1_629:0.0,4_850:0.0):0.006326318)0.975:0.025637393);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000809_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000809_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..233bd2b18b02e887cc421225c347187341cb8e7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000809_tree_id.txt
@@ -0,0 +1 @@
+(2_1960:0.015755075,4_852:0.009414535,(1_631:0.015698108,(0_903:0.010952680,3_1856:0.526407328)0.732:0.004954039)0.846:0.006206516);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000810_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000810_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c8307991650d4f81ae465f5af24f85c4eabcd028
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000810_tree_id.txt
@@ -0,0 +1 @@
+(0_904:0.020249929,4_853:0.003823071,(1_632:0.007951309,(2_1959:0.042959855,3_1855:0.666197020)0.975:0.090828004)0.935:0.016301868);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000811_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000811_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b1a5ca8cb346fc5e22817ec500e3abd5b9948c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000811_tree_id.txt
@@ -0,0 +1 @@
+(1_633:0.012165873,3_1854:0.324651414,(4_854:0.012026037,(2_1958:0.167649516,0_905:0.000000005)0.586:0.005990581)0.823:0.009147218);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000813_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000813_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e12dec623186e70835396119b6b2b3908f3e40ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000813_tree_id.txt
@@ -0,0 +1 @@
+(2_1955:0.166614772,3_1852:0.548185945,((0_907:0.0,4_856:0.0):0.021486419,1_635:0.017863614)0.702:0.058091706);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000814_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000814_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a5792e3091c0129144a0a0457e2a5936c9b5f14e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000814_tree_id.txt
@@ -0,0 +1 @@
+(0_908:0.002078463,1_636:0.009990926,(4_857:0.005540737,(2_1954:0.072133974,3_1851:0.047830354)0.968:0.018605135)0.422:0.004661126);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000817_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000817_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e45749a85815541e0ecf3f66d7451d4e19318178
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000817_tree_id.txt
@@ -0,0 +1 @@
+(3_1841:0.085459254,1_643:0.004241867,(0_921:0.000000005,(2_1890:0.122269769,4_867:0.000000005)0.877:0.009452794)0.788:0.005300972);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000818_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000818_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3f61983468cf76f21e8d5cbccdf6dd8d13f773e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000818_tree_id.txt
@@ -0,0 +1 @@
+(0_922:0.005584674,4_868:0.007464597,(1_644:0.000000005,(2_1889:0.056747643,3_1840:0.226368213)0.995:0.048389773)0.871:0.003728400);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000824_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000824_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ce8066e31f4299797ca06b15e175ed05bcbe0ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000824_tree_id.txt
@@ -0,0 +1 @@
+(4_876:0.008361753,1_652:0.008404289,(0_930:0.003589580,(2_1881:0.043953300,3_1828:0.241418224)0.998:0.081042453)0.816:0.004803917);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000825_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000825_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97fbc8e61df2a990a9a41d3391bf57fc1cfa212a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000825_tree_id.txt
@@ -0,0 +1 @@
+(0_931:0.015712131,4_877:0.003194679,(1_653:0.002078058,(2_1880:0.043743527,3_1827:0.177837278)0.999:0.051991678)0.523:0.006947419);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000826_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000826_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..631d92779d36d1eb2456a279d497022bb13942f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000826_tree_id.txt
@@ -0,0 +1 @@
+(1_657:0.020257824,4_878:0.003195938,(0_935:0.013407912,(2_1878:0.121248370,3_1825:0.246714413)0.994:0.106701297)0.282:0.006789307);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000827_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000827_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5744f8b370200335d79a317c09b70f29f21ad471
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000827_tree_id.txt
@@ -0,0 +1 @@
+(0_936:0.000000005,4_879:0.003255911,(1_659:0.022160474,(2_1877:0.097670699,3_1823:0.282948762)0.973:0.083283367)0.833:0.007749704);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000828_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000828_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..61964c61c072cfc68ac1b2aa83859cc2404f00be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000828_tree_id.txt
@@ -0,0 +1 @@
+(0_937:0.000863419,(2_1876:0.045631684,3_1822:0.141968718)0.971:0.026465705,(1_660:0.006527880,4_880:0.002176841)0.637:0.008213854);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000830_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000830_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..899bf4d120adb9f248240151734fcd7dfb5444df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000830_tree_id.txt
@@ -0,0 +1 @@
+(2_1874:0.012938530,3_1820:0.066080414,(0_939:0.004436495,(1_662:0.0,4_882:0.0):0.000000005)0.937:0.023302501);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000833_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000833_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..545367ac3c9b3da9d1dbdadabbf90f6186fa2c1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000833_tree_id.txt
@@ -0,0 +1 @@
+((0_942:0.0,1_665:0.0,4_885:0.0):0.004519659,2_1870:0.331485101,3_1817:0.035476768);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000834_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000834_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f4e71b01d6abfbe7168f230482f48ccc8507c1d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000834_tree_id.txt
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+(3_1815:0.009466691,(0_943:0.003471733,1_666:0.002098317)0.252:0.001480735,(2_1869:0.163334699,4_886:0.000000005)0.884:0.002452833);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000835_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000835_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e74af48af4b04ba28b18dc8eb22abcf1f44733a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000835_tree_id.txt
@@ -0,0 +1 @@
+(2_1868:0.173735760,3_1814:0.003404819,((0_944:0.0,4_887:0.0):0.000000005,1_667:0.003657497)0.671:0.003897544);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000839_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000839_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee57f38282876cff6d70e8ba4855c44f31d42345
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000839_tree_id.txt
@@ -0,0 +1 @@
+((0_948:0.0,3_1810:0.0,4_891:0.0):0.000000005,1_671:0.006392492,2_1864:0.006408438);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000840_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000840_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0d3afbed0d0194a758f569f50add3db2bf82861
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000840_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000845_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000845_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65679e343aef39cee6e18dd08130d8b0693e4ea6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000845_tree_id.txt
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+(0_956:0.003739970,1_679:0.000000005,(4_899:0.003768662,(2_1856:0.104878497,3_1802:0.140789995)0.991:0.040195372)0.764:0.001835051);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000847_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000847_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0e949edda2d0e8a7c9c7529bf2ff3905184d80d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000847_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000848_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000848_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ebad563c56c2f2e6eb188f97a875845768855c4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000848_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000851_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000851_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..803d1a6863d19e128e4eb408e3a09e54aecd3af7
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000851_tree_id.txt
@@ -0,0 +1 @@
+((0_963:0.0,1_686:0.0,4_906:0.0):0.052141904,2_1850:0.024239464,3_1777:0.117675060);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000854_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000854_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4bb603dcdb7b33c8bf59524132ddc8c63956ca3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000854_tree_id.txt
@@ -0,0 +1 @@
+(2_1847:0.039227708,3_1774:0.219920056,((0_966:0.0,1_689:0.0):0.000000005,4_909:0.013157774)0.965:0.122199563);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000855_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000855_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06bf8e53206eefe24894d98f411b6b72c12b8d93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000855_tree_id.txt
@@ -0,0 +1 @@
+((0_967:0.0,1_690:0.0):0.000000005,4_910:0.018433140,(2_1846:0.048626704,3_1773:0.210217232)0.853:0.020119811);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000861_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000861_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..767714625784eaeca8c706af8540c38ca9bc42f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000861_tree_id.txt
@@ -0,0 +1 @@
+(4_922:0.002700913,(2_1832:0.115317666,3_1723:0.559482654)0.987:0.130199836,(0_978:0.017524610,1_701:0.013349466)0.922:0.018397206);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000864_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000864_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ab9b87dba2d56b30d81dc1ce597ffc4dd23134b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000864_tree_id.txt
@@ -0,0 +1 @@
+(1_704:0.012314427,2_764:1.037965669,(4_925:0.000000005,(0_981:0.000000005,1_705:0.005359698)0.953:0.017483265)0.759:0.023244631);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000865_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000865_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88bbfebbdba79fb07f39e52a83b1c48905284225
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000865_tree_id.txt
@@ -0,0 +1 @@
+(1_706:0.000000005,(2_1829:0.102348742,3_1721:0.180967348)0.992:0.160972121,(0_982:0.000000005,4_926:0.010411218)0.918:0.010469796);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000867_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000867_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ec2eefb6f8b2911089ce5cf5510430b383c729d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000867_tree_id.txt
@@ -0,0 +1 @@
+(2_1824:0.024627123,3_1713:0.247921411,(0_984:0.006531868,(1_708:0.0,4_928:0.0):0.000000005)0.947:0.053344111);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000868_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000868_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f3d938b180ce82df726c8fe84d15bd0279f87d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000868_tree_id.txt
@@ -0,0 +1 @@
+((0_985:0.0,1_709:0.0):0.000825360,4_929:0.003266227,(2_1823:0.016838418,3_1712:0.078800896)0.840:0.010435156);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000870_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000870_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ee3a39c8a6bbda4c52c4fbd94ceb7df9bd23b46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000870_tree_id.txt
@@ -0,0 +1 @@
+((2_1815:0.014041857,3_1704:0.004983051)0.607:0.002051791,1_714:0.013976899,(4_934:0.000000005,0_990:0.003471387)0.280:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000877_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000877_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6538346e3e74ca5ed3a97e5abc87c5cfd6b56597
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000877_tree_id.txt
@@ -0,0 +1 @@
+(0_1003:0.000000005,4_944:0.009502888,(1_725:0.009562737,(2_1809:0.026254749,3_1695:0.248249649)0.945:0.061964475)0.789:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000878_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000878_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..243df5cb8f53925df79f4ece86e07390a3ce8646
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000878_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000882_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000882_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52a48dc623d2d799219ae748c77a83e1819de251
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000882_tree_id.txt
@@ -0,0 +1 @@
+(1_730:0.000000005,4_949:0.005732896,(0_1008:0.000000005,(2_1801:0.101830669,3_1690:0.222902923)0.997:0.126469578)0.877:0.011594835);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000883_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000883_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..01da6661c2de485584140a3f2a7ebbff3cb218cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000883_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000887_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000887_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54ea63d20c4ea253d1fa02e52d35ca140da6d22d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000887_tree_id.txt
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+(1_741:0.000000006,4_960:0.015076980,(0_1013:0.005109130,(2_1796:0.109913833,3_1685:0.236267496)0.920:0.048328215)0.483:0.004929428);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000891_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000891_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c04e720eac8b24fb7d6d885a9e0ee86aa575efaf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000891_tree_id.txt
@@ -0,0 +1 @@
+(0_1017:0.000000005,1_745:0.004461171,(4_964:0.000000005,(2_1792:0.059028274,3_1681:0.123898491)0.961:0.049011367)0.835:0.004451698);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000893_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000893_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b24bee84dc57d8325295856b9cd9b065024eddf
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000893_tree_id.txt
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+(0_1021:0.000000006,(1_749:0.0,4_968:0.0):0.006015747,(2_1789:0.060264229,3_1677:0.146361658)0.868:0.043548549);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000894_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000894_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e9d4439ff1f252a66f6dca516252575010ada88c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000894_tree_id.txt
@@ -0,0 +1 @@
+((0_1033:0.0,1_761:0.0,4_982:0.0):0.002502344,2_1788:0.008922145,3_1674:0.105700733);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000896_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000896_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..820d14c8e16509fba310e7460187b2a0ed7667d8
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000896_tree_id.txt
@@ -0,0 +1 @@
+(2_1786:0.023623728,3_1672:0.119962917,(0_1035:0.007367466,(1_763:0.0,4_984:0.0):0.003928700)0.957:0.029152988);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000897_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000897_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0e2c0d49ca4ea94bb80c589df54b712852bdd69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000897_tree_id.txt
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+(0_1036:0.007836031,(1_764:0.0,4_985:0.0):0.000000005,(2_1784:0.098044320,3_1671:0.220911016)0.909:0.087301315);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000898_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000898_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f45432e97f65138f244fb869e907f05cf6c383f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000898_tree_id.txt
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+(0_1037:0.014811955,(1_765:0.0,4_986:0.0):0.002507206,(2_1783:0.044204726,3_1670:0.164641294)0.976:0.032657034);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000900_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000900_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9be222bfc91d979dbfb460c475418878488c710
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000900_tree_id.txt
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+(0_1039:0.000000005,(1_767:0.0,4_988:0.0):0.009158091,(2_1781:0.115447764,3_1668:0.389481825)0.941:0.093855304);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000901_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000901_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9cd1331261502b93d74b65ee2e0cdb381f62595a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000901_tree_id.txt
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+(2_1780:0.024586369,3_1667:0.208460964,(0_1040:0.007232578,(1_768:0.0,4_989:0.0):0.000000005)0.891:0.019894461);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000905_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000905_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15bb91bc2410619b68fcc6c31a50097f36ed6889
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000905_tree_id.txt
@@ -0,0 +1 @@
+((0_1044:0.0,1_772:0.0,4_993:0.0):0.060726039,2_1775:0.269083939,3_1663:0.045571253);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000906_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000906_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e109e39b340ab5feb8f73116c7d04e9ffaf133b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000906_tree_id.txt
@@ -0,0 +1 @@
+(0_1045:0.002071087,1_773:0.000000005,(4_994:0.000000005,(2_1774:0.326613145,3_1662:0.058067584)0.979:0.043917832)0.844:0.002073795);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000909_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000909_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c080f32d93847f2bad8bc05e18d8f2db3eb6d43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000909_tree_id.txt
@@ -0,0 +1 @@
+(1_776:0.000000006,4_997:0.001022367,(0_1048:0.001534757,(2_1770:0.126203857,3_1659:0.183670622)1.000:0.110318867)0.608:0.000510911);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000910_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000910_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..958de4f0b40e29d5e325e8a2eb1b3ee829a39815
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000910_tree_id.txt
@@ -0,0 +1 @@
+((0_1049:0.0,1_777:0.0,4_998:0.0):0.046967752,2_1769:0.205806535,3_1658:0.291822515);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000913_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000913_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7854d6d92e9cfa9bb62900117185a53ff0355876
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000913_tree_id.txt
@@ -0,0 +1 @@
+((0_1052:0.0,1_780:0.0,4_1001:0.0):0.088598795,2_1766:0.085287220,3_1655:0.134013742);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000914_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000914_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5cc756032039a3f26cbf614ae61ca580d97894ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000914_tree_id.txt
@@ -0,0 +1 @@
+((0_1053:0.0,1_781:0.0):0.000000005,4_1002:0.053126958,(2_1765:0.031645413,3_1654:0.160484577)0.994:0.118961581);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000915_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000915_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf8c9afd3fe423211507001b3e19dd03bd244369
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000915_tree_id.txt
@@ -0,0 +1 @@
+(1_782:0.011337072,(2_1764:0.067323401,3_1653:0.316046743)0.996:0.131534123,(0_1054:0.005579571,4_1003:0.017189184)0.804:0.011210918);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000916_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000916_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09fbffcd9d2956df6c2e344f8d866ca21a88804b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000916_tree_id.txt
@@ -0,0 +1 @@
+(0_1055:0.007455368,4_1004:0.006401995,(1_783:0.002129630,(2_1763:0.040860956,3_1652:0.168719531)1.000:0.049942677)0.285:0.001106483);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000917_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000917_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..109844054e7cb079baf01bc693ab9c654772c061
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000917_tree_id.txt
@@ -0,0 +1 @@
+((0_1057:0.0,1_785:0.0,4_1006:0.0):0.008698549,2_1760:0.014360085,3_1650:0.031247982);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000919_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000919_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bf49bb793ffd06608da723f95cb63c42acf578a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000919_tree_id.txt
@@ -0,0 +1 @@
+(0_1059:0.004344042,(1_787:0.0,4_1008:0.0):0.004185332,(2_1758:0.128886821,3_1648:0.552649297)0.992:0.147079556);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000923_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000923_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..503bfebbb7cb28a34aeb377455da0094f6549b01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000923_tree_id.txt
@@ -0,0 +1 @@
+(0_1064:0.028845942,(1_792:0.0,4_1013:0.0):0.007110234,(2_1751:0.436008188,3_1643:0.652600456)0.965:0.173283600);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000925_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000925_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2483c512a253f593d3d532327c72a52700ea0584
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000925_tree_id.txt
@@ -0,0 +1 @@
+(1_796:0.000000005,4_1018:0.002259376,(0_1068:0.002694415,(2_1748:0.023820840,3_1640:0.103708919)0.960:0.015153634)0.365:0.002959783);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000927_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000927_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a027d63d3565085aa6023bce9ffc4c13d30612d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000927_tree_id.txt
@@ -0,0 +1 @@
+(0_1070:0.005492043,3_1638:0.220736762,(2_1746:0.026639039,(1_798:0.0,4_1020:0.0):0.017504812)0.651:0.007577897);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000929_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000929_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2339870e3996386bf0f5db3e1b170042517c6f7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000929_tree_id.txt
@@ -0,0 +1 @@
+((0_1074:0.0,1_802:0.0,4_1024:0.0):0.077654273,2_1742:0.054827643,3_1634:0.230976495);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000932_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000932_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58d283f06f03bdc4caa886c1a4deac63f30547ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000932_tree_id.txt
@@ -0,0 +1 @@
+((0_1077:0.0,1_805:0.0,4_1027:0.0):0.018100334,2_1739:0.024911376,3_1631:0.031693128);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000934_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000934_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed01af9202f7a1858b3d28c48a3072ab76d40064
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000934_tree_id.txt
@@ -0,0 +1 @@
+(0_1079:0.000000005,1_807:0.004755161,(4_1029:0.000000005,(2_1736:0.041367921,3_1629:0.148198793)0.986:0.031143280)0.461:0.002374916);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000935_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000935_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4569169f56b3b7f09a454e3992da68429cc8409b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000935_tree_id.txt
@@ -0,0 +1 @@
+(0_1080:0.003755529,1_808:0.000000005,(4_1030:0.000000005,(2_1735:0.046336550,3_1628:0.173325842)0.996:0.080106553)0.894:0.007531686);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000936_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000936_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9b5f3393d3df1d348110df653a4a37694df40b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000936_tree_id.txt
@@ -0,0 +1 @@
+(2_1734:0.061232596,3_1627:0.271124256,((0_1081:0.0,1_809:0.0):0.000000005,4_1031:0.011755480)0.963:0.107960528);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000937_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000937_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53fd4d2d9890fa292220e7bbf0ae3b07afbf3132
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000937_tree_id.txt
@@ -0,0 +1 @@
+((0_1082:0.0,1_810:0.0,4_1032:0.0):0.033789478,2_1733:0.025213021,3_1626:0.203950159);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000942_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000942_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53b10e1247e67942608288f70d338acb7b860753
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000942_tree_id.txt
@@ -0,0 +1 @@
+(2_1728:0.042457680,3_1621:0.139048069,((0_1087:0.0,1_815:0.0):0.000000005,4_1037:0.003079187)0.963:0.035153439);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000944_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000944_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..373f5122c8c7294129a2e9baffd680e729e17bb8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000944_tree_id.txt
@@ -0,0 +1 @@
+((0_1089:0.0,1_817:0.0):0.000000005,4_1039:0.003957266,(2_1726:0.067180049,3_1619:0.199985604)0.960:0.055514303);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000945_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000945_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d07c0f89988a3733b5ba72eda53a21bd57ad8b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000945_tree_id.txt
@@ -0,0 +1 @@
+((0_1090:0.0,1_818:0.0):0.000000005,4_1040:0.009709583,(2_1725:0.035943698,3_1618:0.304038301)0.979:0.049735288);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000946_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000946_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65f20342f3569fcabd0e02243351138283e9281f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000946_tree_id.txt
@@ -0,0 +1 @@
+((0_1091:0.0,1_819:0.0,4_1041:0.0):0.029497804,2_1724:0.080763276,3_1617:0.323319789);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000947_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000947_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e785c0240882c361a04cdd1304caedb5cac1187
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000947_tree_id.txt
@@ -0,0 +1 @@
+(1_820:0.001986881,4_1042:0.000000005,(0_1092:0.001986992,(2_1723:0.014685740,3_1616:0.044398461)0.959:0.015875221)0.739:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000950_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000950_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7edc8c2705639a685511d8fb7b446c3639367d90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000950_tree_id.txt
@@ -0,0 +1 @@
+(2_1720:0.009332436,3_1613:0.050699352,(0_1095:0.000000005,(1_823:0.0,4_1045:0.0):0.018748839)0.741:0.009378314);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000951_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000951_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ed8bb3680f1eaff4b38ce2ecdd19b357677d9af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000951_tree_id.txt
@@ -0,0 +1 @@
+(0_1096:0.010430911,(1_824:0.0,4_1046:0.0):0.005425776,(2_1718:0.071367398,3_1612:0.227356153)1.000:0.094927978);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000954_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000954_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d751faefda14a69159c82e67ac7023a649596d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000954_tree_id.txt
@@ -0,0 +1 @@
+(1_828:0.000000005,4_1050:0.006503649,(0_1100:0.011601667,(2_1715:0.189068223,3_1608:0.437480331)0.889:0.097814587)0.813:0.021394702);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000958_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000958_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a1159f251c16e464f8b2a7b8dae6f298edbdb60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000958_tree_id.txt
@@ -0,0 +1 @@
+(0_1105:0.000000005,(1_833:0.0,4_1055:0.0):0.003568196,(2_1710:0.260894778,3_1603:0.109546679)0.970:0.073997826);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000959_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000959_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b78d888a75c443c345e19c3964736e897284d474
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000959_tree_id.txt
@@ -0,0 +1 @@
+((0_1107:0.0,1_835:0.0,4_1057:0.0):0.011402006,2_1707:0.011805741,3_1601:0.011629412);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000960_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000960_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03cf655e4ab84bcdbf93cfa690b2c6d5895df151
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000960_tree_id.txt
@@ -0,0 +1 @@
+((0_1108:0.0,1_836:0.0,4_1058:0.0):0.072647734,2_1705:0.037267786,3_1600:0.248992210);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000962_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000962_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bfe615e68d954bf80ab50f6a4e2c7dbe7db6e231
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000962_tree_id.txt
@@ -0,0 +1 @@
+((0_1111:0.0,1_839:0.0,4_1061:0.0):0.010868934,2_1701:0.010898936,3_1598:0.110699696);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000965_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000965_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4d7ec9740af2d0a96b133c8d8d6169793c112b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000965_tree_id.txt
@@ -0,0 +1 @@
+(0_1115:0.002213381,4_1065:0.004441762,(1_843:0.005072557,(2_1698:0.039657967,3_1594:0.130670323)1.000:0.062415398)0.826:0.003982755);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000969_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000969_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53f8096ea72d4ee86c83f98320e0a7689bd315df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000969_tree_id.txt
@@ -0,0 +1 @@
+(0_1119:0.004486845,1_847:0.002246647,(4_1069:0.000000005,(2_1693:0.055262532,3_1590:0.262611345)0.990:0.045659084)0.848:0.006780514);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000971_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000971_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..309b4f6814ad5aafb8222c0ca6814fd6ec82e2c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000971_tree_id.txt
@@ -0,0 +1 @@
+((0_1121:0.0,1_849:0.0,4_1071:0.0):0.009657466,2_1691:0.048767598,3_1588:0.115959564);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000973_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000973_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c14a6a84e0bab95bc10be2a04b4f923a55cceeaf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000973_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000977_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000977_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ab4b1830109362d3b6221cf565ce1c0733ea6472
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000977_tree_id.txt
@@ -0,0 +1 @@
+(1_855:0.002803893,4_1077:0.000000005,(0_1127:0.005608309,(2_1685:0.025331929,3_1582:0.151457516)0.876:0.013282102)0.995:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000980_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000980_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5de62e6a23e0522b0cb568faac2eef1352f2217
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000980_tree_id.txt
@@ -0,0 +1 @@
+(0_1130:0.015265786,1_858:0.004998295,(4_1080:0.000000005,(2_1682:0.034982025,3_1579:0.502462734)0.627:0.016871975)0.932:0.015353699);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000982_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000982_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed25175bc675c4e2ee2c1d9dfcafddf723ae0647
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000982_tree_id.txt
@@ -0,0 +1 @@
+(2_1680:0.000000005,4_1082:0.015761227,((0_1132:0.0,1_860:0.0):0.015604939,3_1577:0.227985557)0.723:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000983_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000983_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66905080905242a5a3985747cc349c08b713e177
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000983_tree_id.txt
@@ -0,0 +1 @@
+(0_1133:0.010713839,4_1083:0.002137923,(1_861:0.002142880,(2_1679:0.067093038,3_1576:0.179246060)0.979:0.032061180)0.752:0.002121447);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000985_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000985_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd3635ac6cd5eadac2ea4278d3efc9542678dc6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000985_tree_id.txt
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+(0_1136:0.007747889,4_1086:0.003880628,(1_864:0.010055941,(2_1675:0.111028159,3_1573:0.455581312)0.997:0.071391635)0.155:0.004744720);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000986_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000986_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c5e969eb9bdc858f9d5fd3283aa98e071502832
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000986_tree_id.txt
@@ -0,0 +1 @@
+((0_1137:0.0,1_865:0.0,4_1087:0.0):0.046189582,2_1674:0.030374311,3_1572:0.420206078);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000988_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000988_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..634a888517d1b9c442d29a9d143804237edc2bc4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000988_tree_id.txt
@@ -0,0 +1 @@
+(0_1139:0.000000005,4_1089:0.000996967,(1_867:0.015219016,(2_1672:0.042188090,3_1570:0.214038577)1.000:0.045130550)0.959:0.008102686);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000990_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000990_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..955201a0f40477d41a97c27c1937e530e7f8c739
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000990_tree_id.txt
@@ -0,0 +1 @@
+((0_1141:0.0,1_869:0.0,4_1091:0.0):0.009183213,2_1670:0.032102292,3_1568:0.105965441);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000992_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000992_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e191b363ce90c50aa60ec0a86d73925a84cab886
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000992_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000993_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000993_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91e6212734f5bbeb2f27064f28ad4ef389cf3e39
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000993_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000994_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000994_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..100f2ec56383f90bf1468e463cffc129359a787c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000994_tree_id.txt
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+(1_873:0.009789719,4_1095:0.002786537,(0_1145:0.000000006,(2_1666:0.099150882,3_1564:0.317682870)1.000:0.097542874)0.922:0.004170184);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000995_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000995_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fbbf52a4912a087f5299e866499cd081765ff340
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000995_tree_id.txt
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+(0_1146:0.016323374,4_1096:0.000000006,(1_874:0.013620300,(2_1665:0.141002136,3_1563:0.629793954)0.959:0.129161327)0.745:0.008253675);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000996_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000996_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4dc61fc2590f8f6da3bafc79dd132a6447eeb7e
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001000_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001000_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3cef28e4a1b66eb2c2b859d87c3597685f221901
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001000_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001003_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001003_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca6111cec6bb3026a4ac2c39987b37d26b638dfb
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001004_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001004_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f1643d179122cc0f31983a307f1a473a91b544f
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@@ -0,0 +1 @@
+(2_1654:0.050015147,3_1551:0.215029987,(1_884:0.021958501,(0_1156:0.023740353,4_1113:0.017537739)0.982:0.082578143)0.953:0.065313986);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001005_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001005_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae3f227493b414393f5ee7c31ad3d8ca84ad0b56
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+(0_1157:0.029423670,1_885:0.009485802,(4_1114:0.001100544,(2_1653:0.002837774,3_1550:0.037262980)1.000:0.030858278)0.703:0.006245055);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001007_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001007_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8fb53d091ffd28bb923dc09db9798c290f85cd6a
--- /dev/null
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+(2_1651:0.023148024,3_1548:0.031608933,((0_1159:0.0,1_887:0.0):0.000000005,4_1116:0.007742818)0.778:0.007875497);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001011_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001011_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8712c187945c729b4022c813517b4e1efc286eb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001011_tree_id.txt
@@ -0,0 +1 @@
+(0_1163:0.011217167,4_1120:0.000000005,(1_891:0.007303408,(2_1647:0.113931370,3_1544:0.777732853)0.831:0.041305858)0.842:0.009537000);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001012_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001012_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f7da5266ff8e1a28e0ed4b7cfda60a0c643d57f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001012_tree_id.txt
@@ -0,0 +1 @@
+((0_1164:0.0,4_1121:0.0):0.006914536,1_892:0.003257964,(2_1646:0.009843054,3_1543:0.130660176)0.944:0.024809806);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001013_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001013_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e09595404efabff492991194d1220f4a7a995dd1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001013_tree_id.txt
@@ -0,0 +1 @@
+(0_1166:0.001711833,4_1123:0.000000005,(1_894:0.004612789,(2_1645:0.019960765,3_1541:0.075645825)0.991:0.034213903)0.719:0.002260744);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001014_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001014_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d19a094c088d1a21c66a44403ce30507e4c3ca5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001014_tree_id.txt
@@ -0,0 +1 @@
+(1_895:0.000000005,4_1124:0.003113775,(0_1167:0.003119721,(2_1644:0.029149251,3_1540:0.161951425)0.977:0.030965517)0.779:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001016_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001016_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a31991496bd5fbf191a5500de9a7e17d63e1683d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001016_tree_id.txt
@@ -0,0 +1 @@
+((0_1169:0.0,1_897:0.0,4_1126:0.0):0.033318973,2_1642:0.064461428,3_1538:0.109082420);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001018_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001018_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..947a0829270cf049afd1d6e472e902007558774e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001018_tree_id.txt
@@ -0,0 +1 @@
+(1_899:0.003860631,4_1129:0.000000005,(0_1171:0.000000005,(2_1640:0.059268631,3_1536:0.237717887)0.996:0.082352581)0.843:0.003845959);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001020_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001020_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..556f801bbca32ecb071031c1fe9636bbb0878142
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001020_tree_id.txt
@@ -0,0 +1 @@
+(0_1173:0.005717012,4_1131:0.000000005,(1_901:0.000000005,(2_1638:0.038825839,3_1534:0.163842915)0.997:0.063436147)0.941:0.008574427);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001021_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001021_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee0d942ee90eeb506cc909fb59e48ca64974b539
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001021_tree_id.txt
@@ -0,0 +1 @@
+(1_902:0.007156995,4_1132:0.003550935,(0_1174:0.000000005,(2_1637:0.079590647,3_1533:0.125066278)0.939:0.038213324)0.804:0.003529335);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001024_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001024_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5d22bfca4e7bf929c18c418b399f8c7a83104bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001024_tree_id.txt
@@ -0,0 +1 @@
+((2_1633:0.112993391,3_1530:0.394382020)0.996:0.212818008,4_1136:0.000000005,(1_906:0.028834358,0_1178:0.004478332)0.936:0.014359690);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001025_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001025_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4184ebe56f3b2da93ddd6996e23ad711f4662158
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001025_tree_id.txt
@@ -0,0 +1 @@
+(0_1179:0.000000005,(1_907:0.0,2_1632:0.0,4_1137:0.0):0.010451641,3_1529:0.053251860);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001026_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001026_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49eb71047d82e49e1a29bedf92f49443a9b2934c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001026_tree_id.txt
@@ -0,0 +1 @@
+(2_1631:0.050945576,3_1528:0.187288716,(0_1180:0.004018448,(1_908:0.0,4_1138:0.0):0.007642513)0.991:0.048294398);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001028_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001028_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ea0d6f3cb945457d15ac655ff9736372fe8c1e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001028_tree_id.txt
@@ -0,0 +1 @@
+(1_910:0.000000005,4_1140:0.000000005,(0_1182:0.013362939,(2_1629:0.298819014,3_1526:0.522780928)0.970:0.154927817)0.992:0.063261909);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001031_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001031_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3511ebc4ffd4d9cf26b351440bc7543c70fae4bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001031_tree_id.txt
@@ -0,0 +1 @@
+(0_1185:0.005303633,4_1143:0.006617795,(1_913:0.010550686,(2_1626:0.064740465,3_1523:0.197580940)1.000:0.123815388)0.867:0.009704422);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001032_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001032_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0303d5d4487fc7df12d3b8a6e2e2a48097bd9911
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001032_tree_id.txt
@@ -0,0 +1 @@
+(0_1186:0.034747608,1_914:0.027231821,(4_1144:0.012800248,(2_1625:0.128228928,3_1522:0.234753828)0.987:0.098766615)0.909:0.014572246);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001035_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001035_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..249b46cd14b27101f8549d5a1f875f2816831dc1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001035_tree_id.txt
@@ -0,0 +1 @@
+(1_917:0.000000005,4_1147:0.002250639,(0_1189:0.013822137,(2_1622:0.085300189,3_1519:0.242286057)0.958:0.036013888)0.929:0.016456205);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001039_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001039_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ecbd9050d9085e3c71864b89a2d4312dc5d11bec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001039_tree_id.txt
@@ -0,0 +1 @@
+(0_1193:0.003336054,4_1151:0.000000005,(1_921:0.000000005,(2_1618:0.066345516,3_1515:0.271168764)0.993:0.112055106)0.874:0.003336635);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001040_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001040_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db1e36a2b4b533dead4f2b186850b03e123ae362
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001040_tree_id.txt
@@ -0,0 +1 @@
+((0_1194:0.0,4_1152:0.0):0.000000005,1_922:0.000884569,(2_1617:0.022386335,3_1514:0.074258033)0.992:0.016948360);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001041_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001041_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e96b33d1ca9f2d23859d341da628fa9b830bf3c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001041_tree_id.txt
@@ -0,0 +1 @@
+((0_1195:0.0,4_1153:0.0):0.002550496,1_923:0.002476245,(2_1616:0.031950245,3_1513:0.180829152)0.976:0.031647285);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001045_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001045_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e5cd8affff63a5370d7bc119cfb40e9beccb3fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001045_tree_id.txt
@@ -0,0 +1 @@
+((0_1199:0.0,1_927:0.0,4_1157:0.0):0.035728412,2_1611:0.019543675,3_1508:0.094841653);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001048_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001048_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7efc9a90253921df4a90f3a2175b037bd572d4e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001048_tree_id.txt
@@ -0,0 +1 @@
+(0_1202:0.006284634,(1_930:0.0,4_1160:0.0):0.006735582,(2_1608:0.053014428,3_1505:0.609786038)0.979:0.110847699);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001050_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001050_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c74ac38a4778d97423272dd8b0ea86f2d16f1b9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001050_tree_id.txt
@@ -0,0 +1 @@
+(0_1204:0.017577742,(1_932:0.0,4_1162:0.0):0.011627159,(2_1606:0.087598869,3_1503:0.336536041)0.994:0.097550451);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001051_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001051_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91b8cc9e0b4ccdad988016b09a317d766443ddca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001051_tree_id.txt
@@ -0,0 +1 @@
+(1_934:0.005726089,4_1163:0.000000005,(0_1206:0.011554214,(2_1604:0.087472053,3_1501:0.333005735)0.682:0.021235363)0.859:0.012159168);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001053_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001053_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2fa364dbe439321baac2993ddb7584851010996f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001053_tree_id.txt
@@ -0,0 +1 @@
+((0_1208:0.0,1_936:0.0,4_1165:0.0):0.194613583,2_1602:0.079897976,3_1499:0.755433207);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001054_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001054_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a25e60172f1ddf42ab2c029adf7ab697cbcdae7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001054_tree_id.txt
@@ -0,0 +1 @@
+(0_1209:0.000000005,(1_937:0.0,4_1166:0.0):0.004778528,(2_1600:0.000000005,3_1498:0.004762801)0.920:0.009588020);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001055_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001055_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b940c865316f6504fc84dcac2f1f0d15a0ae9f3
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001055_tree_id.txt
@@ -0,0 +1 @@
+((0_1210:0.0,1_938:0.0,4_1167:0.0):0.230004577,2_1599:0.119268357,3_1497:0.373507074);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001056_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001056_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0bf000db825e7bbb72fadcfa7dc0c5b8d46f4651
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001056_tree_id.txt
@@ -0,0 +1 @@
+(0_1211:0.003216730,(1_939:0.0,4_1168:0.0):0.005232356,(2_1598:0.049703665,3_1496:0.122425267)0.994:0.045935485);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001058_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001058_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b055e3d03cdb6207565e4f18652fba9079798ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001058_tree_id.txt
@@ -0,0 +1 @@
+(0_1213:0.000000005,(1_941:0.0,4_1170:0.0):0.001656449,(2_1597:0.178208963,3_1494:0.098570828)1.000:0.134968171);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001059_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001059_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dcf5fe84cdd5b2d4c2d4b89aec0107c252cc6475
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001059_tree_id.txt
@@ -0,0 +1 @@
+((0_1214:0.0,1_942:0.0,4_1171:0.0):0.123477277,2_1596:0.147296020,3_1492:0.103556647);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001060_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001060_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0285340dde06ec48a765b766789ecc774c60312a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001060_tree_id.txt
@@ -0,0 +1 @@
+(0_1215:0.000000005,1_943:0.003356438,(4_1172:0.001536469,(2_1594:0.023630374,3_1491:0.065565759)0.998:0.021940265)0.787:0.001845419);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001064_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001064_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ee93813b1a473baba0f8ba957ea354f4cb2555f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001064_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001065_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001065_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9423fac49ad3f8b88add010ca505c9d723f4695
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001065_tree_id.txt
@@ -0,0 +1 @@
+(0_1220:0.009785253,(1_948:0.0,4_1177:0.0):0.009657512,(2_1589:0.043727056,3_1484:0.166013241)0.994:0.029603113);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001068_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001068_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5f58ced339c27bf9e1b7cd9ff4e85f3c7ff5702
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001068_tree_id.txt
@@ -0,0 +1 @@
+(0_1223:0.006839690,(1_951:0.0,4_1180:0.0):0.000000005,(2_1586:0.069354335,3_1481:0.495661590)0.908:0.095282976);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001069_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001069_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3221eda144df5590f33c01c5a6b2ef3b9d3293ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001069_tree_id.txt
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+(0_1225:0.004540169,(1_953:0.0,4_1182:0.0):0.000000005,(2_1584:0.072491966,3_1479:0.207213083)0.941:0.056274369);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001070_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001070_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77781b6fe921d50e7082211ccc822d9e54b58c4e
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001070_tree_id.txt
@@ -0,0 +1 @@
+(2_1583:0.059713301,3_1478:0.172547350,(0_1226:0.004506550,(1_954:0.0,4_1183:0.0):0.000000005)0.907:0.035676180);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001071_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001071_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..448d54beb192897bcda9ca55e774534f0399e6d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001071_tree_id.txt
@@ -0,0 +1 @@
+((0_1227:0.0,1_955:0.0,4_1184:0.0):0.066095005,2_1582:0.061860105,3_1477:0.080947638);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001075_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001075_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..789ac88bf0d1202a6e46cec01df1c74df63a4269
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001075_tree_id.txt
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+(0_1231:0.004868015,(1_959:0.0,4_1188:0.0):0.000000005,(2_1577:0.072954474,3_1472:0.347817801)0.989:0.117127080);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001076_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001076_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1fcade5667dcef741231e22ed3b2b2c5113d66cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001076_tree_id.txt
@@ -0,0 +1 @@
+(1_960:0.004716226,4_1189:0.000000005,(0_1232:0.000000005,(2_1576:0.254276224,3_1471:0.235799277)0.993:0.079870573)0.806:0.002358031);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001077_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001077_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3d06fd41fb012f691e62be0c86c6f398e5a7252
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001077_tree_id.txt
@@ -0,0 +1 @@
+(0_1233:0.008207065,4_1190:0.000000005,(1_961:0.001753124,(2_1575:0.091108290,3_1470:0.204349263)1.000:0.119622954)0.642:0.000974302);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001081_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001081_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d5a3de699fbcd8aca1542c4e8083f66fd5c5695
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001081_tree_id.txt
@@ -0,0 +1 @@
+(2_1569:0.083643425,3_1465:0.400488821,(0_1238:0.023914924,(1_966:0.0,4_1195:0.0):0.010779170)0.974:0.093654367);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001082_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001082_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d7bd71b29686e722440a63b0291e91ba9aad3a6
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@@ -0,0 +1 @@
+(0_1239:0.001454876,1_967:0.000000005,(4_1196:0.002919075,(2_1568:0.038129755,3_1464:0.124964383)0.996:0.032286482)0.925:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001086_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001086_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57fac902fb81d7f145b0e195972c7c62e8d3dc0c
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001091_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001091_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd23b4aea776fbc01017cd02a333ad21133c5165
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001096_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001096_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1eb5e1c54588e471724ff77c787cbba9ba395d2b
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001099_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001099_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a804522c9ba494e2ea368c9c2c4c4caa8938999
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001099_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001102_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001102_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bdeb1ccacf847d05d3c8ef963827e462aa66b0b2
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001103_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001103_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..002e1575c0b8b33af8d00cfd6ef86d2f59559f01
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+(1_1000:0.002755984,4_1225:0.008276775,(0_1270:0.000000005,(2_1544:0.026259049,3_1440:0.163788062)0.970:0.030967734)0.979:0.016747839);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001105_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001105_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb66b49ab5f4e321573d483899568783c864d4cc
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+(2_1541:0.014303831,3_1437:0.220811940,((0_1272:0.0,1_1002:0.0):0.000000005,4_1227:0.013983635)0.877:0.028705172);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001106_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001106_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68f4ae3cd68b31c77ca696e75690c6f711ea5fd1
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001107_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001107_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a403c204130f73704c193fcaed68a3ca1633aee2
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001107_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001108_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001108_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e07448c0dbf005a49290b968076edae5331639e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001108_tree_id.txt
@@ -0,0 +1 @@
+(2_1538:0.084878779,3_1434:0.296535985,((0_1275:0.0,4_1230:0.0):0.006318554,1_1005:0.000000005)0.969:0.057252387);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001109_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001109_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4fe611eded2e3152cc89e86ae0a35eb8b40efc0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001109_tree_id.txt
@@ -0,0 +1 @@
+(0_1276:0.009507959,4_1231:0.003804344,(1_1006:0.000000006,(2_1537:0.100875493,3_1433:0.205429835)0.984:0.043054225)0.929:0.009520773);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001110_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001110_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6b8c53fb7fc72f5dc57926943606269d1d618bba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001110_tree_id.txt
@@ -0,0 +1 @@
+(0_1277:0.002166831,4_1232:0.000000005,(1_1007:0.004334608,(2_1536:0.033287348,3_1432:0.011032053)0.647:0.004232746)0.893:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001112_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001112_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e97201501efb1f5060b657b5d59dcb8680e0896d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001112_tree_id.txt
@@ -0,0 +1 @@
+(1_1009:0.008594932,3_1430:0.182864454,((0_1279:0.0,2_1534:0.0):0.000000005,4_1234:0.008552095)0.710:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001113_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001113_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e0501d6dc9858c3976dcb878fa4546343e1aedc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001113_tree_id.txt
@@ -0,0 +1 @@
+(0_1280:0.000000005,1_1010:0.001797957,(4_1235:0.005428179,(2_1533:0.029696682,3_1429:0.688946089)0.438:0.012879216)0.976:0.010823631);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001115_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001115_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c274c84e8fca6d2719539845275224e1c1f38fb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001115_tree_id.txt
@@ -0,0 +1 @@
+(2_1531:0.021603044,3_1427:0.083016348,((0_1282:0.0,4_1237:0.0):0.000000005,1_1012:0.002996894)0.702:0.002617632);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001116_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001116_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81894030475e8a56b4a28da6d65562be51bf3ead
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001116_tree_id.txt
@@ -0,0 +1 @@
+((2_1530:0.048399841,3_1426:0.373849748)0.987:0.073900469,4_1238:0.003667077,(1_1013:0.003680679,0_1283:0.000000005)0.402:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001118_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001118_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3058b0cd6bb99a52ebaf64ca5f65d94b2f52a7df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001118_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001119_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001119_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a3f880c70d4d8c451aee54e1cd6a50404ea113b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001119_tree_id.txt
@@ -0,0 +1 @@
+(1_1017:0.017416430,4_1242:0.000000005,(0_1287:0.014283924,(2_1526:0.056696887,3_1422:0.296144337)0.997:0.039379272)0.870:0.004150702);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001120_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001120_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62ee8caa8ed36649f0b80a1d89a8193ca14d7a06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001120_tree_id.txt
@@ -0,0 +1 @@
+(0_1288:0.008981793,4_1243:0.004508559,(1_1018:0.000000006,(2_1525:0.013229472,3_1421:0.114780462)0.984:0.024194266)0.962:0.013738784);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001122_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001122_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..801947231ad09c94a1d061d6c61769cc3e827a2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001122_tree_id.txt
@@ -0,0 +1 @@
+(2_1523:0.144502891,3_1419:0.370641033,(0_1291:0.037212171,(1_1020:0.0,4_1245:0.0):0.004881924)0.924:0.146190600);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001123_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001123_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02f94920759f1a8829b114e5159aa2b86eb5cb42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001123_tree_id.txt
@@ -0,0 +1 @@
+(0_1292:0.012676999,4_1246:0.000000005,(1_1021:0.000000005,(2_1522:0.032052962,3_1418:0.126061128)0.963:0.030286281)0.797:0.003156967);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001124_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001124_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37c543fb660e54c05c7f1c9f34517acb36cec798
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001124_tree_id.txt
@@ -0,0 +1 @@
+((0_1294:0.0,1_1023:0.0,4_1248:0.0):0.029530866,2_1520:0.020829829,3_1416:0.082153418);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001125_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001125_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7958830235e58499d73500fe736c31c03dca1c61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001125_tree_id.txt
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+(0_1295:0.000838914,4_1249:0.000838733,(1_1024:0.003117252,(2_1519:0.020057122,3_1415:0.087807038)0.996:0.016807565)0.718:0.001123775);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001126_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001126_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98b1b7aacec478869c6cfea165f5aea8ad002e66
--- /dev/null
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+(0_1296:0.003030144,1_1025:0.009372317,(4_1250:0.005786410,(2_1518:0.111728137,3_1414:0.130031115)0.925:0.023932729)0.884:0.006990565);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001127_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001127_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1bb87210592765d80409a192a0e24dcb83775051
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001127_tree_id.txt
@@ -0,0 +1 @@
+(0_1297:0.006306055,1_1026:0.006196787,(4_1251:0.007261021,(2_1517:0.057330434,3_1413:0.334458382)0.983:0.115465748)0.744:0.005467033);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001128_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001128_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..08e634becc3e88090169f59dca886cbcf74d2058
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001128_tree_id.txt
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+(1_1027:0.035162885,4_1252:0.000000005,(0_1298:0.000000005,(2_1516:0.102241746,3_1412:0.464512137)1.000:0.253342207)0.368:0.014452156);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001130_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001130_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4db42ca83dbca2f9364080e5b416fb3b08db8514
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001130_tree_id.txt
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+(0_1300:0.004607779,4_1254:0.004605136,(1_1029:0.013851789,(2_1514:0.111443393,3_1410:0.260756100)0.973:0.092196893)0.866:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001132_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001132_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ba91a883e45e86dc104463a3917cf5df29618dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001132_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001134_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001134_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c85163ade914befe10b85dce51da7994b7cf9564
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001134_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001135_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001135_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b362d101217c210747fbfae2783ec0fb4b4f6605
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001135_tree_id.txt
@@ -0,0 +1 @@
+(0_1305:0.003902368,1_1034:0.000000005,(4_1259:0.002711505,(2_1509:0.050110125,3_1405:0.149434809)1.000:0.076134261)0.782:0.003166790);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001144_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001144_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca5f6673540491c8af5f06d255847aee5ca8b145
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001144_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001145_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001145_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb91c31ef2a09e3734fb7d9ec6a61cd8f1bce94c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001145_tree_id.txt
@@ -0,0 +1 @@
+((0_1316:0.0,1_1045:0.0,4_1270:0.0):0.163088624,2_1499:0.183884860,3_1394:0.670206763);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001149_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001149_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a8ec1a0ed29f054b29efb590cdf2113e6298ca84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001149_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001150_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001150_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e9fd686ce76c2dc65f4b5d44f206b6358d3aaf8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001150_tree_id.txt
@@ -0,0 +1 @@
+((0_1322:0.0,4_1276:0.0):0.000000005,1_1051:0.002093166,(2_1492:0.016050370,3_1388:0.133793799)0.885:0.007275482);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001151_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001151_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b5b7dd018f33ba75e934c4f5aff7549b122d1fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001151_tree_id.txt
@@ -0,0 +1 @@
+(0_1323:0.000000005,4_1277:0.008568456,(1_1052:0.038967977,(2_1491:0.071341520,3_1387:0.129814235)0.915:0.032028452)0.299:0.004867404);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001157_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001157_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ff78b352d8075076fdca106f851fb1af4c9674a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001157_tree_id.txt
@@ -0,0 +1 @@
+(0_1329:0.005670927,1_1058:0.011605857,(4_1283:0.012066572,(2_1485:0.076898301,3_1380:0.419178263)0.912:0.055476690)0.764:0.005218190);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001158_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001158_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ffced993693d459f9cca5cfc87cb71771df1e7e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001158_tree_id.txt
@@ -0,0 +1 @@
+(1_1059:0.000000005,4_1284:0.008128749,(0_1330:0.009774261,(2_1484:0.106846365,3_1379:0.433640388)0.953:0.080325299)0.934:0.019227145);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001161_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001161_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4596b8ece14e629c815d9b39931a8d66102f10a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001161_tree_id.txt
@@ -0,0 +1 @@
+((0_1333:0.0,4_1287:0.0):0.019709140,1_1062:0.002281174,(2_1481:0.059757363,3_1376:0.195570323)0.997:0.069365908);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001164_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001164_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e8bba3a46e0232d59fd15a6a5d22d22d1704670
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001164_tree_id.txt
@@ -0,0 +1 @@
+((0_1357:0.0,4_1306:0.0):0.000000005,1_1096:0.002507502,(2_1461:0.093416076,3_1372:0.244378445)0.977:0.043508579);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001168_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001168_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..431efcb0ae6149b18687c7decd97eb584c4665c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001168_tree_id.txt
@@ -0,0 +1 @@
+(0_1365:0.001916696,4_1314:0.003853598,(1_1105:0.003823488,(2_1456:0.021696278,3_1363:0.054682102)0.996:0.040339636)0.775:0.001952421);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001170_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001170_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..61b40e43a3e53d89f351462af0ff03d8290604e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001170_tree_id.txt
@@ -0,0 +1 @@
+(1_1107:0.010416981,4_1316:0.000000005,(0_1367:0.007419184,(2_1454:0.015345548,3_1361:0.043536287)0.588:0.013199270)0.446:0.008212217);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001171_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001171_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a33ce4053749f0d2cf9bcfef0a723ef1be709e62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001171_tree_id.txt
@@ -0,0 +1 @@
+(0_1369:0.021456199,2_1452:0.005894610,(1_1109:0.000000005,(3_1360:0.288236871,4_1318:0.026264843)0.790:0.019423808)0.870:0.005926136);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001172_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001172_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47cdd40cae6594cd3c77267f0d2f49fd3f63292a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001172_tree_id.txt
@@ -0,0 +1 @@
+(0_1370:0.008490754,4_1319:0.004274015,(1_1110:0.004599726,(2_1451:0.042314226,3_1359:0.216250222)0.981:0.055359113)0.948:0.025519264);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001175_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001175_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcac7a698c1d5f774086bac01b31a55359e19542
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001175_tree_id.txt
@@ -0,0 +1 @@
+(1_1113:0.003509365,4_1322:0.007080309,(0_1373:0.032690264,(2_1448:0.118362593,3_1356:0.181423561)1.000:0.168734827)0.945:0.021979263);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001177_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001177_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..181f179b448b1a18bf12569ba02f9559a4d03815
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001177_tree_id.txt
@@ -0,0 +1 @@
+(0_1375:0.036400512,(1_1115:0.0,4_1324:0.0):0.000000005,(2_1446:0.144255170,3_1354:0.285505460)0.985:0.100235050);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001180_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001180_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1288b2a5c4c11af69c3239093e3efdfd88bc14bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001180_tree_id.txt
@@ -0,0 +1 @@
+(0_1378:0.004049568,4_1327:0.000000005,(1_1119:0.002052409,(2_1443:0.041380657,3_1350:0.116328688)0.966:0.025473644)0.413:0.004054571);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001183_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001183_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..864881d3110626f3b55949c54be09d240659edfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001183_tree_id.txt
@@ -0,0 +1 @@
+((0_1381:0.0,1_1122:0.0,4_1330:0.0):0.032997992,2_1439:0.054324796,3_1347:0.227454414);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001184_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001184_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..12c06f97d2c85ea2f985a976d843f5a44959dc64
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001184_tree_id.txt
@@ -0,0 +1 @@
+(0_1382:0.000000005,(1_1123:0.0,4_1331:0.0):0.006125977,(2_1438:0.039378725,3_1346:0.117560819)0.985:0.035729327);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001186_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001186_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..afa6f641c75334c58bb28c5ebc13a94bf88bd242
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001186_tree_id.txt
@@ -0,0 +1 @@
+(0_1384:0.002942595,1_1125:0.000000005,(4_1333:0.003012585,(2_1436:0.039729987,3_1344:0.131954709)0.988:0.040817238)0.767:0.002877886);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001187_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001187_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96f15b2abee861df27dab85dc2e228096ccd5812
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001187_tree_id.txt
@@ -0,0 +1 @@
+(0_1385:0.004870343,4_1334:0.009856821,(1_1126:0.002485909,(2_1435:0.055817760,3_1343:0.171327582)1.000:0.095682558)0.452:0.004805423);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001190_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001190_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54ca553194d44476594430b705c38e92f08bbaa9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001190_tree_id.txt
@@ -0,0 +1 @@
+(2_1431:0.042215547,3_1339:0.374863659,(0_1389:0.004479308,(1_1130:0.0,4_1338:0.0):0.000000005)1.000:0.116208860);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001192_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001192_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e710cd98a2c8baab19f688e5d569b108b7c40d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001192_tree_id.txt
@@ -0,0 +1 @@
+(0_1391:0.001139371,1_1132:0.001141259,(4_1340:0.008457401,(2_1429:0.048476527,3_1337:0.305847895)1.000:0.053315650)0.963:0.008784960);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001194_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001194_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d4e5e7de9495a6558830e24dec512c491b885c7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001194_tree_id.txt
@@ -0,0 +1 @@
+(0_1394:0.027914098,4_1343:0.006962291,(1_1135:0.000000006,(2_1427:0.109260646,3_1331:0.264362105)0.994:0.139229643)0.446:0.006939511);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001197_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001197_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..456ad6f3eb415156daa25b1eadc073b592e4d02e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001197_tree_id.txt
@@ -0,0 +1 @@
+(2_1424:0.165299426,3_1328:0.377163383,((0_1397:0.0,1_1138:0.0):0.015162482,4_1346:0.000000006)0.965:0.107452434);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001200_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001200_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41af0d22a6501ba62d8c8aea282b5b5632a24c9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001200_tree_id.txt
@@ -0,0 +1 @@
+((0_1402:0.0,1_1143:0.0,4_1351:0.0):0.015384407,2_1420:0.015593799,3_1323:0.031760791);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001202_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001202_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aabd1faa1b306492a788550ca83af90e7973a78a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001202_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001203_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001203_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0f879e4d4f089fe69568a923a03492b994b9936
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001203_tree_id.txt
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+(0_1405:0.000000005,(1_1146:0.0,4_1354:0.0):0.006216566,(2_1417:0.201189528,3_1320:0.675879846)0.987:0.248437260);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001206_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001206_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..994a2ef17a24a9eade30ef87324d66947295f6bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001206_tree_id.txt
@@ -0,0 +1 @@
+(0_1408:0.007530763,(1_1149:0.0,4_1357:0.0):0.015221916,(2_1414:0.183003051,3_1317:0.549956987)1.000:0.206546418);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001209_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001209_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e54816b42ec5bc88f5ec8936cb074e9b64df5593
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001209_tree_id.txt
@@ -0,0 +1 @@
+(1_1152:0.016199705,4_1360:0.000000005,(0_1411:0.000000005,(2_1411:0.142971035,3_1314:0.591143487)0.996:0.225110424)0.901:0.010826006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001210_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001210_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..549234e14983b6f0db458cd788ba76b4592527a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001210_tree_id.txt
@@ -0,0 +1 @@
+((0_1412:0.0,4_1361:0.0):0.000000005,1_1153:0.019981024,(2_1410:0.204919031,3_1313:0.519721192)0.997:0.219410764);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001213_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001213_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5bec99223c34b847965d9dc5b122b4cd8855ec38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001213_tree_id.txt
@@ -0,0 +1 @@
+(0_1415:0.004305463,1_1156:0.000000005,(4_1364:0.007766449,(2_1407:0.059643459,3_1309:0.324634246)0.156:0.039218445)0.748:0.005140703);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001216_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001216_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a37e88feeb5f065ce5591a11cb4b9f69057d17c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001216_tree_id.txt
@@ -0,0 +1 @@
+(2_1403:0.035002793,3_1305:0.101715299,((0_1419:0.0,4_1368:0.0):0.014019077,1_1160:0.008571126)0.925:0.024719707);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001219_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001219_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2397ec852cda48631ba207e9732cae0918db946
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001219_tree_id.txt
@@ -0,0 +1 @@
+(0_1422:0.002663654,1_1163:0.000000006,(4_1371:0.000000005,(2_1400:0.038261475,3_1302:0.142580014)0.975:0.037031345)0.888:0.008019740);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001220_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001220_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae57dbfc393e19e777167a14eb9e13261d2b5fef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001220_tree_id.txt
@@ -0,0 +1 @@
+(0_1423:0.014693603,(1_1164:0.002418169,4_1372:0.000000006)0.962:0.012004260,(2_1399:0.154315819,3_1301:0.008805084)0.782:0.004431074);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001223_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001223_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d9347a9324daeb8f5aa9dd07cb14236bbf58d03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001223_tree_id.txt
@@ -0,0 +1 @@
+(1_1169:0.003157608,4_1377:0.003152943,(0_1428:0.003166170,(2_1396:0.116651428,3_1296:0.319770891)0.994:0.101253437)0.794:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001224_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001224_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b49a136c795549e3dc2c9d7d0812de1c77ca10a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001224_tree_id.txt
@@ -0,0 +1 @@
+((0_1429:0.0,4_1378:0.0):0.009677687,1_1170:0.006721116,(2_1395:0.044161032,3_1295:0.146634067)0.952:0.066784877);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001230_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001230_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c1a1810c3d7f5403e760547c91cee8a1ac3db290
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001230_tree_id.txt
@@ -0,0 +1 @@
+((2_1389:0.022154722,3_1288:0.193611421)0.993:0.053801295,4_1384:0.000000005,(0_1435:0.006365120,1_1176:0.000000006)0.423:0.004231354);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001232_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001232_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..484ee665f1749f43c374d5e66efc59889103e28c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001232_tree_id.txt
@@ -0,0 +1 @@
+(0_1459:0.002824863,4_1386:0.005659890,(1_1178:0.002821152,(2_1387:0.129864275,3_1286:0.449066629)0.979:0.085048617)0.777:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001233_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001233_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..95649b2e4b7d098b5e68b5c286cb9c3fec395d1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001233_tree_id.txt
@@ -0,0 +1 @@
+((0_1461:0.0,1_1180:0.0):0.018971780,4_1388:0.003404512,(2_1385:0.245573101,3_1285:0.489418461)0.925:0.086814380);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001234_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001234_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20115f19c8d6f4cba90d0223fac4a0a964343d04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001234_tree_id.txt
@@ -0,0 +1 @@
+(0_1462:0.004115494,1_1181:0.000000005,(4_1389:0.006806125,(2_1384:0.263296203,3_1284:0.984711687)0.805:0.074932165)0.893:0.013909548);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001236_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001236_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..388ed37a8665aa774c66f7a197a03cf50ce471a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001236_tree_id.txt
@@ -0,0 +1 @@
+(0_1464:0.003030669,1_1183:0.000000005,(4_1391:0.010392567,(2_1382:0.085959157,3_1282:0.467053352)0.978:0.074895298)0.775:0.005314786);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001240_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001240_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e10359aeda7161d91818b0922bfc67873f87afb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001240_tree_id.txt
@@ -0,0 +1 @@
+(0_1468:0.007541953,1_1187:0.007519666,(4_1395:0.015226905,(2_1378:0.036416114,3_1278:0.467789245)0.997:0.250163007)0.773:0.007675426);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001241_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001241_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..acb361728742b23480225bf5147d2aefde158e73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001241_tree_id.txt
@@ -0,0 +1 @@
+(0_1469:0.008426911,4_1396:0.008359168,(1_1188:0.008577330,(2_1377:0.038996293,3_1277:0.236280736)0.950:0.042404856)0.835:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001244_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001244_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..530ce2d527d6b2a4f6047a964dece8609f2cae75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001244_tree_id.txt
@@ -0,0 +1 @@
+((2_1374:0.023687430,3_38:0.292323046)0.878:0.013852263,4_1399:0.003760517,(0_1472:0.015675277,1_1191:0.013231790)0.744:0.002939625);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001245_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001245_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44bc76b8564770201a2de7068356862c10602701
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001245_tree_id.txt
@@ -0,0 +1 @@
+((0_1473:0.0,4_1400:0.0):0.007573218,1_1193:0.000462712,(2_1373:0.010757152,3_1265:0.345443791)0.864:0.015028397);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001250_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001250_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d4dafabd9673522e344ebde0c6ec5639b4c113f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001250_tree_id.txt
@@ -0,0 +1 @@
+((0_1478:0.0,1_1198:0.0,4_1405:0.0):0.057146449,2_1368:0.083355762,3_1260:0.160267648);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001253_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001253_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aaf6c47f7f2c708baad91f960c8e55550324a27c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001253_tree_id.txt
@@ -0,0 +1 @@
+(0_1481:0.006437362,1_1201:0.000000005,(4_1408:0.006562189,(2_1365:0.091053915,3_1257:0.222127860)0.998:0.073162420)0.624:0.002057374);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001261_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001261_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20745361926e49b3da3fcc0275aeabe84619f3cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001261_tree_id.txt
@@ -0,0 +1 @@
+((0_1490:0.0,1_1210:0.0):0.002288152,4_1417:0.004824994,(2_1356:0.026597175,3_1248:0.146228949)0.989:0.032841641);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001265_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001265_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b9e920c8677c2f7ffbd70a3c27b4696e89de5c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001265_tree_id.txt
@@ -0,0 +1 @@
+(0_1494:0.000000005,1_1214:0.003372000,(4_1421:0.002279692,(2_1352:0.156515483,3_1244:0.949112413)0.966:0.135939763)0.888:0.011316438);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001267_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001267_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47c19677301ad6d0783c383847795f230e758366
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001267_tree_id.txt
@@ -0,0 +1 @@
+(4_1424:0.049876789,1_1217:0.000000005,(0_1497:0.004768881,(2_1349:0.114153220,3_1241:0.446863002)0.985:0.222253508)0.699:0.011617936);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001274_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001274_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57f630dab6e460f8f5fa34d140c6d54c7ccdd8e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001274_tree_id.txt
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+(0_1504:0.002998980,4_1431:0.000000005,(1_1224:0.009048029,(2_1342:0.027017299,3_1234:0.088902833)1.000:0.103251737)0.894:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001279_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001279_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..00eb0821ca85b56d099f70e64fac07d06eff4f73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001279_tree_id.txt
@@ -0,0 +1 @@
+(0_1511:0.006272866,4_1438:0.003113343,(1_1231:0.000000005,(2_1336:0.046748110,3_1228:0.163469041)0.968:0.031949840)0.670:0.003105115);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001281_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001281_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0a4553b27010069f527b30d3ce79937a0d6c922
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001281_tree_id.txt
@@ -0,0 +1 @@
+(4_1440:0.002314994,3_1226:0.300522980,((0_1513:0.0,1_1233:0.0):0.004010429,2_1334:0.003993350)0.282:0.001672651);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001282_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001282_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b689e6b06e096981030e4b805e92b794ae81f3e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001282_tree_id.txt
@@ -0,0 +1 @@
+((0_1514:0.0,1_1234:0.0):0.013564771,4_1441:0.019119579,(2_1333:0.027398074,3_1225:0.267205995)0.926:0.013946637);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001287_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001287_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1668d954c09822b6d5c8446dd7a34375f45b50a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001287_tree_id.txt
@@ -0,0 +1 @@
+((2_1325:0.152542548,3_1219:0.271320810)0.940:0.095279848,1_1240:0.005580974,(0_1520:0.000000005,4_1447:0.005613103)0.751:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001288_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001288_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b5643a75b5630a9f18988fe8542332bc783e413
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001288_tree_id.txt
@@ -0,0 +1 @@
+((0_1521:0.0,1_1241:0.0):0.000000005,4_1448:0.005714327,(2_1324:0.135904116,3_1218:0.135342730)0.923:0.141086355);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001290_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001290_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..716ccae643347a7745947ffb36df155a2671a168
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001290_tree_id.txt
@@ -0,0 +1 @@
+(4_1450:0.010837187,(2_1321:0.100699075,3_1215:0.129413257)0.985:0.058401010,(0_1523:0.003605997,1_1243:0.010753302)0.594:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001293_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001293_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..330797f59c7ae47dc2047a489f751f4b5e365869
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001293_tree_id.txt
@@ -0,0 +1 @@
+(2_1318:0.169446176,3_1212:0.000000005,(0_1526:0.009352219,(1_1246:0.000000005,4_1453:0.003116849)0.939:0.009366607)0.944:0.009354089);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001294_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001294_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..011e8acd4c4402469931a33262f919eb029b85f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001294_tree_id.txt
@@ -0,0 +1 @@
+(1_1254:0.002320320,4_1460:0.000000005,(0_1533:0.004637829,(2_1310:0.034677799,3_1209:0.383635636)0.955:0.033313214)0.898:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001297_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001297_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3737bd3d00642824fab4188df6154d04a8552c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001297_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001298_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001298_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef44cd700f90c16526c0b7fb3686e48ee4620051
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001298_tree_id.txt
@@ -0,0 +1 @@
+(4_1468:0.024530737,3_1190:0.020038872,(1_1263:0.002824627,(0_1541:0.009061482,2_1276:0.390601167)0.680:0.010500567)0.225:0.007482294);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001301_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001301_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..342bbff4716c1e7d60f027d35786a87810e5324e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001301_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001302_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001302_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b63013e021fab74fe17ad583569d7974cbb60f28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001302_tree_id.txt
@@ -0,0 +1 @@
+(1_1268:0.000000005,4_1473:0.006038829,(0_1546:0.000000005,(2_1268:0.018714153,3_1178:0.012992403)0.994:0.050887803)0.796:0.012281223);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001304_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001304_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6156706b3cee850578e8b3f3b1198689aeee2615
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001304_tree_id.txt
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+(2_1266:0.008803064,3_1175:0.013364722,((0_1549:0.0,4_1476:0.0):0.000000005,1_1271:0.008816271)0.770:0.004376883);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001306_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001306_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb635e3f06230097241551f5bdd0ac3651212197
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001306_tree_id.txt
@@ -0,0 +1 @@
+(2_1262:0.039364812,(0_1557:0.016746463,3_1168:0.016778297)0.777:0.005541167,(1_1278:0.011204562,4_1483:0.000000005)0.799:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001308_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001308_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f52f3efaa76b0c6e33647d2535b25799bd657b1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001308_tree_id.txt
@@ -0,0 +1 @@
+(1_1599:0.014191232,3_819:0.017815295,(2_880:0.016497369,(0_1566:1.562202798,4_1820:0.010255697)0.758:0.009314131)0.347:0.005399709);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001310_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001310_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3247a8649edae6b8f0c3472f979d072a88e0c90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001310_tree_id.txt
@@ -0,0 +1 @@
+(0_1574:0.010810288,4_1503:0.016048580,(1_1289:0.024966974,(2_1243:0.163186503,3_1152:0.042870965)0.970:0.064684291)0.878:0.025557652);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001311_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001311_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5552e332d1345ee71c80aa39da48902725d424f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001311_tree_id.txt
@@ -0,0 +1 @@
+(0_1575:0.013618208,1_1290:0.006810124,(4_1504:0.006784799,(2_1242:0.072061673,3_1151:0.340402069)0.924:0.071477842)0.401:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001312_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001312_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d17a62c5a2e247d5439129cb313e66e67f0ff3d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001312_tree_id.txt
@@ -0,0 +1 @@
+(0_1576:0.011796024,4_1505:0.007040507,(1_1291:0.004680105,(2_1241:0.041585274,3_1150:0.272280497)0.992:0.054543059)0.871:0.004768712);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001313_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001313_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc904cf76c2cacee3346c4aa80dad585a28e758f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001313_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001314_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001314_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53133ab7d594d3a73f24e4291b6c2af78c3d6ef0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001314_tree_id.txt
@@ -0,0 +1 @@
+(1_1293:0.012967804,4_1507:0.000000005,(0_1578:0.003360299,(2_1238:0.051413000,3_1148:0.086438681)0.860:0.022020319)0.495:0.009685027);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001319_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001319_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a771a5d71e59eab65774cd28957fde484887384
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001319_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001320_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001320_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1136ac71662bf9a68b40f9052ef5cfc1dfa111f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001320_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001322_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001322_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..102b827af765b35cabd557ac3079d59cdbd52e98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001322_tree_id.txt
@@ -0,0 +1 @@
+(1_1302:0.016600102,4_1517:0.004960554,(0_1587:0.000000005,(2_1229:0.080845925,3_1139:0.522339766)0.999:0.105365257)0.836:0.001634172);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001324_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001324_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b21ef96d156fdcfc884f3c6ddfed3990210b05fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001324_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001325_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001325_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee60db48777bfa8ee2dde9a91d6980a01855e13d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001325_tree_id.txt
@@ -0,0 +1 @@
+(0_1590:0.009786783,4_1520:0.004858386,(1_1305:0.000000005,(2_1224:0.068527258,3_1136:0.219369768)0.887:0.027901712)0.792:0.009764784);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001326_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001326_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c49290ce35b138ad0aaa6e6fcc8cc4412cb1542d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001326_tree_id.txt
@@ -0,0 +1 @@
+(1_1306:0.008976528,4_1521:0.000000005,(0_1591:0.000000005,(2_1223:0.104390539,3_1135:0.522990062)0.900:0.052897443)0.714:0.008953370);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001327_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001327_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f67cf34834f7f7bb412f532b71502da87d437b60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001327_tree_id.txt
@@ -0,0 +1 @@
+(1_1307:0.009969882,4_1522:0.000000005,(0_1592:0.010072189,(2_1222:0.160745861,3_1134:0.195446181)0.942:0.087779771)0.913:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001329_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001329_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..230bdff2bd1c249f4a59b113eaa8ce9bfe4ec74d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001329_tree_id.txt
@@ -0,0 +1 @@
+(0_1594:0.003065866,4_1524:0.009498830,(1_1309:0.003559349,(2_1220:0.059677012,3_1132:0.269726352)1.000:0.053163758)0.916:0.005138815);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001330_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001330_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5df87021425d22061d63d52099545719d599c3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001330_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001332_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001332_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eaf1811a57760adec92558cfb11af5d51810632a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001332_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001333_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001333_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a5eb2b312294d3621856e9cb89c60927e401b65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001333_tree_id.txt
@@ -0,0 +1 @@
+(0_1598:0.007827191,4_1528:0.002607758,(1_1313:0.005215678,(2_1216:0.018041593,3_1128:0.093861701)0.990:0.027602995)0.760:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001335_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001335_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ab2edf82c3e99553e11f75ffc8c70a582c3521e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001335_tree_id.txt
@@ -0,0 +1 @@
+(0_1600:0.012366139,4_1530:0.000000005,(1_1315:0.000000005,(2_1214:0.073042126,3_1126:0.121926244)1.000:0.060643228)0.844:0.002043207);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001339_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001339_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f6d5bdde3b69d8a772bf51861da9d7c5071589c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001339_tree_id.txt
@@ -0,0 +1 @@
+(0_1607:0.004386286,3_1120:0.006979609,(4_1537:0.006995097,(1_1322:0.002136597,2_1208:0.101591965)0.903:0.010804157)0.370:0.002831032);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001340_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001340_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e90d8a09377fdc85bac2ad067141dbc1323fcf55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001340_tree_id.txt
@@ -0,0 +1 @@
+(1_1323:0.008352643,4_1538:0.010375228,(0_1608:0.008097122,(2_1207:0.186563848,3_1119:0.073670799)0.958:0.035118782)0.721:0.002740387);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001342_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001342_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b70a66b92f1560435b850e1b85483dce7a01620
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001342_tree_id.txt
@@ -0,0 +1 @@
+(0_1610:0.000000006,(2_1205:0.070662755,3_1117:0.120486140)1.000:0.256595601,(4_1540:0.007424599,1_1325:0.009910945)0.246:0.002429442);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001343_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001343_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52b5b7a37d6b5f2c52d3ca1fd1db43c08e5087e4
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001343_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001344_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001344_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca5f8694f8cbfdd85035c68c93413f59ca4bd881
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001344_tree_id.txt
@@ -0,0 +1 @@
+(1_1327:0.008579611,4_1542:0.002889415,(0_1612:0.003891061,(2_1203:0.017128481,3_1115:0.159818874)0.934:0.018260115)0.900:0.013478708);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001345_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001345_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..51381a9c77a386296532e865db5ae78ffc0b85b6
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001345_tree_id.txt
@@ -0,0 +1 @@
+(2_1202:0.061871259,3_1114:0.381374510,(0_1613:0.024493069,(1_1328:0.0,4_1543:0.0):0.005830341)0.950:0.071897576);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001346_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001346_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37ba33af5ae797228af90a0c3952b53eb3fcf600
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001346_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001347_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001347_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06ff9d5bae67d6f8a051727e9032c94a873e677e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001347_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001348_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001348_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63053980d95e18c04a8f66070a0d0250ec0f204b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001348_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001350_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001350_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2731ed753a4ee06f106bab4fbd845173f9fff06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001350_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001354_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001354_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30d06d33289be58b7408c5fffce61295b45e274f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001354_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001355_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001355_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe3a5f0d21076b2e5fb8be87d08039e8050340e0
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001355_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001356_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001356_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40fd34c27519912a9c691aec793e74fe8578a874
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001360_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001360_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..220417e7d25dec8beaffa4a9a06261a6d0edcbb6
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001364_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001364_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2f5a35d91c61cad7b158428f8a6e6f9b603e623
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001364_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001366_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001366_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5636ad3da1af22bd0201dab2c0e7d38f01e7dc3
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001366_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001368_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001368_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ac79a2d6ef6d0394b0394f243bcb850288151778
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001368_tree_id.txt
@@ -0,0 +1 @@
+((0_1641:0.0,1_1358:0.0,2_1158:0.0,4_1570:0.0):0.016408159,3_1089:0.016408159);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001369_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001369_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..efab807707c881d896f92649190af69953be73f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001369_tree_id.txt
@@ -0,0 +1 @@
+((0_1642:0.0,1_1359:0.0,2_1157:0.0,4_1571:0.0):0.014730978,3_1088:0.014730978);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001371_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001371_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..923b7192fb4c39384b6e45888b43f793cdb5f481
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001371_tree_id.txt
@@ -0,0 +1 @@
+(1_1361:0.000000005,4_1573:0.007017100,(0_1644:0.003547229,(2_1155:0.035757367,3_1086:0.150200137)0.995:0.070246971)0.866:0.007008065);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001372_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001372_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13523a1c79acaee409ea04827b8d5d9433a5554e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001372_tree_id.txt
@@ -0,0 +1 @@
+(1_1362:0.004752232,4_1574:0.004730575,(0_1645:0.000000005,(2_1154:0.015692952,3_1085:0.155277980)0.949:0.043791321)0.859:0.009566028);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001373_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001373_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0cf2b70078e785aa2a5fc2e3c7f94aee04630ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001373_tree_id.txt
@@ -0,0 +1 @@
+(2_1153:0.030122511,3_1084:0.105395101,((0_1646:0.0,1_1363:0.0):0.006772420,4_1575:0.002457346)0.999:0.044628454);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001374_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001374_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5011ffea99f8f30e2b67b04ad7c07e7d1c428e31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001374_tree_id.txt
@@ -0,0 +1 @@
+((0_1647:0.0,1_1364:0.0,4_1576:0.0):0.013413849,2_1152:0.006491811,3_1083:0.091276311);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001378_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001378_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4d491cd20357071d9831327f8543a5e6d9f3dbb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001378_tree_id.txt
@@ -0,0 +1 @@
+(2_1148:0.000501605,3_1079:0.102692584,(0_1651:0.000000005,(1_1368:0.0,4_1580:0.0):0.005538897)0.781:0.010652887);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001380_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001380_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0208fdd74ac1dcd3b1b543c77a5efe77194a276
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001380_tree_id.txt
@@ -0,0 +1 @@
+((0_1653:0.0,1_1370:0.0,4_1582:0.0):0.013786726,2_1146:0.013127799,3_1077:0.030631992);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001381_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001381_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a0d066114afced2eca5f251d9824862ccd5fcc53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001381_tree_id.txt
@@ -0,0 +1 @@
+((0_1654:0.0,1_1371:0.0,4_1583:0.0):0.017421744,2_1145:0.017400055,3_1076:0.036281006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001382_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001382_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c89c2d4e2f5914811df18511f5dcdd664af08ce
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001382_tree_id.txt
@@ -0,0 +1 @@
+((0_1655:0.0,1_1372:0.0,2_1144:0.0,4_1584:0.0):0.008035521,3_1075:0.008035521);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001385_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001385_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..378be81413af897278bc6d1a8e29a870624d392d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001385_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001389_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001389_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..23d101c8d8a35ad86162adc06695b7ce3cc2fba1
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001389_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001391_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001391_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..539a4f52d48f988fe4c0cecaf93222981395d8b5
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001391_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001392_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001392_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..889325e3dcf68d7ae0840903b229d71dc93afd6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001392_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001393_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001393_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..041c4e53e029ff2b24dc1d663609559e71cf022f
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001393_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001395_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001395_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3cdb29e1a27b20155c96bf7b9d399e07923fa66b
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001397_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001397_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f999844635f569c97614e6878c4d4ef935bb6f97
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001397_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001398_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001398_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ac9202c8e34b1aa243ed398d65486ab459aa7bbf
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001398_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001401_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001401_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..527695fdaba94e2b625ce510ee5f7784775bcaee
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001401_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001402_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001402_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ee32dd6c7b16f4ee5813dee4029351056378ee4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001402_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001404_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001404_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ae41b7f20160c653898680d0ae702b5f71cc6aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001404_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001413_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001413_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ce5e15d708c67fdbc99646744a0963b511459a51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001413_tree_id.txt
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+(1_1403:0.003910704,4_1615:0.000000005,(0_1686:0.000000005,(2_1112:0.170578081,3_1042:0.985974726)0.935:0.133260109)0.468:0.003907939);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001414_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001414_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f6f9e4015015139dba31e6e45b28a58a8591b74e
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001415_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001415_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5bc0cdf12f20b50bfc69f6108349c53a9a43f162
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@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001416_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001416_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e9fd30078942fed9ac891dff6aab74e08a68f261
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001416_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001419_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001419_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be0fb9512b0bf17cd4afa3dfc36d5a5cac62cd3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001419_tree_id.txt
@@ -0,0 +1 @@
+(2_1106:0.100011873,3_1035:0.365971755,((0_1692:0.0,1_1409:0.0):0.012101197,4_1621:0.000000005)0.993:0.087642762);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001421_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001421_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..71bd4939179ac78e442ae9ea8562ee1d790f2dad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001421_tree_id.txt
@@ -0,0 +1 @@
+((0_1694:0.0,1_1411:0.0,4_1623:0.0):0.003994091,2_1104:0.030352802,3_1030:0.101288846);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001422_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001422_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53620dc869cc96eccc829be8e89c2beb78a541bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001422_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001423_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001423_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2388b549f20e76f541c4e3c829d7f0f062823227
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001423_tree_id.txt
@@ -0,0 +1 @@
+(2_1102:0.058421230,3_1028:0.332415933,((0_1696:0.0,1_1413:0.0):0.004952131,4_1625:0.035363437)0.873:0.099725757);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001424_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001424_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5abd7300473f616da7d5ad59a938fa5bba2105c
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001424_tree_id.txt
@@ -0,0 +1 @@
+(2_1101:0.070852324,3_1027:0.090651856,((0_1697:0.0,1_1414:0.0):0.009830124,4_1626:0.002876645)0.997:0.059745797);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001426_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001426_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6b5d4218a30131077d8ca1104f5bba9d54d9eb2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001426_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001429_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001429_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df396a393c5856a898b97108eaad8a0abcb4e699
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001429_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001431_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001431_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..768c60621090dc1cf22c16e401e9d752969984e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001431_tree_id.txt
@@ -0,0 +1 @@
+(2_1094:0.052729720,3_1020:0.088048216,((0_1704:0.0,1_1421:0.0):0.005189604,4_1633:0.002239404)0.998:0.045683419);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001432_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001432_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0bfb833990cf698d39103d866dbabf2f21279252
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001432_tree_id.txt
@@ -0,0 +1 @@
+(0_1705:0.002331424,1_1422:0.000000005,(4_1634:0.000000005,(2_1093:0.138834264,3_1019:0.101086773)0.962:0.038455384)0.915:0.002329368);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001436_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001436_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4c8832e693c8374a0daffbd550eb89deb44d2dfd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001436_tree_id.txt
@@ -0,0 +1 @@
+(0_1710:0.005877232,4_1639:0.000000005,(1_1427:0.005879510,(2_1088:0.000000005,3_1015:0.092113770)0.907:0.011984605)0.462:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001440_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001440_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae517b9c555baf40e4d56eb805c712ab38a73968
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001440_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001443_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001443_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e429320c6d0d10a5541bd41b0cfab19080040827
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001443_tree_id.txt
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+(1_1435:0.002162059,4_1647:0.004314762,(0_1718:0.006508698,(2_1080:0.041841401,3_1005:0.177402257)0.998:0.072968476)0.770:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001444_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001444_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1fc0a46c6efb342b9b499f0e55cd570647601c4e
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001444_tree_id.txt
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+(1_1436:0.001496188,4_1648:0.006046568,(0_1719:0.015299260,(2_1079:0.093116798,3_1004:0.316418343)0.998:0.107759267)0.794:0.003006542);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001445_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001445_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c124e5bcf3b2b6116c627593e36203de1b623de9
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001445_tree_id.txt
@@ -0,0 +1 @@
+(0_1723:0.000000005,4_1652:0.003521994,(1_1440:0.004351007,(2_1076:0.169566258,3_1000:0.741453645)0.914:0.086000422)0.845:0.009921826);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001447_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001447_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5ab599c362d37899ae528ce7f8bf2d25cea9eb4
--- /dev/null
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+(0_1725:0.000000005,1_1442:0.002815062,(4_1654:0.008476210,(2_1074:0.032844963,3_998:0.057188896)0.859:0.011546942)0.860:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001449_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001449_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ae6f430d64e87bd02ef8baccc224fd520d0382c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001449_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001450_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001450_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a498e90b603a128807d08b171262cc0e6902a1d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001450_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001452_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001452_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd58f2bc5e4f49363f86a6ee3a38648055d5d388
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001452_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001455_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001455_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..007b4d43b51c546fc8d90efab578dc57604920c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001455_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001456_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001456_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..514eeacb7273f1618cb5fadc0975076c55c35b7a
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001458_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001458_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..794dedf2a627d20e394ced71eed63d5183379b6c
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@@ -0,0 +1 @@
+(2_1046:0.000000005,3_982:0.426198614,(4_1670:0.000000005,(0_1748:0.008538954,1_1456:0.004258958)0.833:0.000000005)0.868:0.004241633);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001462_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001462_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..abdf3cb476e71c9a43c207643d81974f775ad78c
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001464_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001464_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6018174407a67cd62e58641cb404f8f8b3e0c8e
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001465_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001465_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb04f8617af797abe317c1cd09c25d2e6f316a5d
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+(0_1757:0.010395251,4_1679:0.000000005,(1_1465:0.004570477,(2_1033:0.186738109,3_972:0.240573281)1.000:0.236439890)0.787:0.005835275);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001466_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001466_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..674b8a7567d41a878405835563c6848de6b593ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001466_tree_id.txt
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+(1_1466:0.037548266,4_1680:0.000000005,(0_1758:0.003337997,(2_1032:0.068759620,3_971:0.195410165)0.986:0.067713099)0.730:0.003309135);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001468_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001468_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64a7b4b3be6dc58ba6147f5059447dba21f174f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001468_tree_id.txt
@@ -0,0 +1 @@
+(1_1468:0.000000005,4_1682:0.002083533,(0_1760:0.003152095,(2_1030:0.036654137,3_969:0.085407816)0.997:0.029743750)0.757:0.001017703);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001471_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001471_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49067138939c1e98713361230f306c4e30a74dc1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001471_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001472_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001472_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4f8dd0942608169d6e5d5e780cf189ebef0cab7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001472_tree_id.txt
@@ -0,0 +1 @@
+(0_1764:0.007851118,4_1686:0.004525904,(1_1472:0.010800365,(2_1025:0.103729058,3_965:0.144925463)1.000:0.057930901)0.767:0.002531104);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001473_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001473_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c465eb7e39b28279ea1d4c5f1a6d1606ee157e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001473_tree_id.txt
@@ -0,0 +1 @@
+(0_1765:0.006364589,4_1687:0.013221101,(1_1473:0.019347916,(2_1024:0.247232853,3_964:0.571180370)0.809:0.061986509)0.881:0.020168801);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001475_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001475_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a83f7341b8efaa3c6942595e1821cc043a12cb2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001475_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001476_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001476_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..902cb559386bf9a274ca9421fb09ce7bfc3dbd29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001476_tree_id.txt
@@ -0,0 +1 @@
+(0_1768:0.009217491,4_1690:0.012211917,(1_1476:0.014028252,(2_1021:0.169153735,3_961:0.630731035)0.939:0.081087481)0.893:0.017427907);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001480_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001480_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..025446e052adf90901036bab7c122651ce95d446
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001480_tree_id.txt
@@ -0,0 +1 @@
+(1_1481:0.000000005,4_1695:0.003087591,(0_1773:0.000000005,(2_1015:0.026980981,3_956:0.089299632)1.000:0.034789538)0.927:0.003081780);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001482_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001482_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7468a6a452d8d060c0c8be8a2f517424a65ef831
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001482_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001484_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001484_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b047b18750d39b54082f796b12841819c22eab2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001484_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001487_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001487_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..854f65b25280db522c6572758385eb871257cfcc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001487_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001488_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001488_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a243f71460bf64f69e59c6fd1aa9110d675df233
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001488_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001489_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001489_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..defac9995a96b5ea74c0d87a6420551117f55578
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001489_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001491_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001491_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ac8d42ab4cac1bae5c508fbac083e2647fece045
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001491_tree_id.txt
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+((0_1788:0.0,1_1495:0.0,4_1709:0.0):0.032482673,2_1000:0.045646837,3_943:0.155801458);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001492_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001492_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6692138124d01aa95992e2076952fc6990592cd2
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001496_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001496_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4b834cf20b5cabc9b2720e5a2656fc6d94a0aaf
--- /dev/null
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+(0_1794:0.005388996,1_1501:0.008307843,(4_1715:0.003231237,(2_994:0.193816300,3_937:0.161009272)1.000:0.135991630)0.081:0.005078130);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001497_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001497_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16e329d8919ff8de5988ecd8696c49a13cf3fa46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001497_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001499_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001499_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..08ab125212c1e2fcffbfd8c35201c371ddfab214
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001499_tree_id.txt
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+(0_1797:0.003677311,4_1718:0.001842089,(1_1504:0.006439672,(2_987:0.054075311,3_932:0.077386094)1.000:0.078136093)0.633:0.000930012);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001500_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001500_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b6fb403227598267308f846e8d8383526a9c7c57
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001503_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001503_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d216ede0cf42ca9387d67b15d34c496f89659fe
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001505_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001505_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..776d9f3fa9d9d12bb629b3ec6abc8de1c0bf21f6
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001507_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001507_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f6bcf673d5aa5ece9a2fc5f96d0fe87e5b435c5c
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001512_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001512_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..89fd97f8b6ad3c6b95c8fcb8d840c80bfcdd22da
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001513_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001513_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06d31e1119b77995e1360cc9a40d413146325991
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001513_tree_id.txt
@@ -0,0 +1 @@
+(4_1732:0.033195255,(2_969:0.395322193,3_908:0.537933930)0.989:0.132383400,(0_1811:0.010253691,1_1518:0.000000005)0.807:0.010778336);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001516_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001516_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b7480ac2d9223d82099d2875a6599d11600d40b
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001516_tree_id.txt
@@ -0,0 +1 @@
+(2_966:0.005599642,4_1735:0.010401590,((0_1814:0.0,1_1521:0.0):0.071329700,3_904:0.436699833)0.881:0.041378766);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001519_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001519_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a0903b6ff5f12ba3a79cf6e4c7618b1a7d4bb183
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001519_tree_id.txt
@@ -0,0 +1 @@
+(0_1817:0.008124035,2_962:0.004345069,(3_901:0.048257355,(1_1524:0.004711459,4_1738:0.004641667)0.807:0.003566471)0.361:0.003216429);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001525_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001525_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b6cb3dc830be68201cea574a89c760a6ec571bfd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001525_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001528_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001528_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e169ca4a4c6616a6ec2cc3885c1b3e0624164dd1
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001528_tree_id.txt
@@ -0,0 +1 @@
+(0_1829:0.110766730,4_1750:0.000000005,(1_1536:0.000000005,(2_949:0.038756895,3_888:0.412069228)0.968:0.094230547)0.948:0.016299201);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001529_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001529_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ac46903b1d4eef515f888ff57dd93406d532265
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001529_tree_id.txt
@@ -0,0 +1 @@
+(0_1830:0.009468371,1_1537:0.022912211,(4_1751:0.001917519,(2_948:0.023362519,3_887:0.268390031)0.998:0.034953773)0.986:0.013521266);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001531_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001531_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0bdd864709e3dc6d9e0708ee72ecd7991ff5bfff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001531_tree_id.txt
@@ -0,0 +1 @@
+(1_1539:0.005260079,(2_946:0.024423225,3_885:0.141622010)0.879:0.021985834,(0_1832:0.005225719,4_1753:0.000000005)0.739:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001532_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001532_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b369a3402881adc540899f1e7f9b64c1868dac14
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001532_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001533_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001533_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f14777e51c5eefc6e09394052c6b01b9a1c7fff5
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+(0_1839:0.025096565,4_1760:0.006162920,(1_1546:0.000000005,(2_939:0.096626812,3_880:0.447358238)0.817:0.061782185)0.786:0.006225013);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001537_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001537_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52db868ba96e7c9ededf7df931e896fcb7f14afe
--- /dev/null
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+(0_1843:0.013891521,4_1764:0.005977385,(1_1550:0.006519560,(2_935:0.054406138,3_876:0.210657659)0.996:0.055663071)0.725:0.005933811);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001539_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001539_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ddb762c58f56f8393d21dd795821bd3a6e496676
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001539_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001540_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001540_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bf3161ab0aefb33e3c8e9451a1b090ea36ed4461
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001541_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001541_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..196cc509a976050b6148d0de6566bdf468ede6d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001541_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001542_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001542_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86c75693f5a932e2af7f877930fdca4f4481d32e
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001542_tree_id.txt
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+((0_1848:0.0,1_1555:0.0,2_930:0.0,4_1769:0.0):0.034943607,3_871:0.034943607);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001543_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001543_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03bcb5ea5c0c6ea73ba32d07db7e702a22b12aca
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+((0_1849:0.0,1_1556:0.0,4_1770:0.0):0.008888451,(2_929:0.0,3_870:0.0):0.008888451);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001548_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001548_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..631b6b6df7cc9733ef5bdcaa27ca43b1665d3955
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001553_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001553_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5d203175cf485e7349da5553256ae71b58d496d
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001555_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001555_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa84eeb109cd231563b4420073eaa42b6942430d
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001556_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001556_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52b94e18873111b58aedf2f2450e17ea9c8bb73a
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001558_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001558_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10ea6002dc1c67f1161aa587cc9690dc014985d2
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001560_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001560_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2705da6f0d2709230bdcfbbfb059d52373a2dc10
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001561_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001561_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..038dc58fc98a8f3fa7db88179bd59bc716cd05a0
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001563_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001563_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e9b3f838bde693a02820e8274cb92b36d722636e
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001564_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001564_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1aadc2c5d1274408f33900daf005cb5a895063f5
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001565_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001565_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..518db149c966c79e7186bb82051ee9d7e12fe3ac
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001566_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001566_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c99928fa033af555225aeacc47f1f805de322463
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+(3_832:0.009241792,(1_1590:0.000000005,4_1803:0.003710446)0.866:0.003776705,(2_893:0.078070804,0_1883:0.008635670)0.380:0.002563902);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001567_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001567_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca27f11151ddf45580dc8630837e683981797492
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001567_tree_id.txt
@@ -0,0 +1 @@
+(4_1804:0.004991758,2_892:0.022620010,(0_1884:0.002481520,(1_1591:0.000000005,3_831:0.012594315)0.880:0.004983527)0.789:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001569_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001569_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d28be800450e7f7c763ab6847a4a929508e95e6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001569_tree_id.txt
@@ -0,0 +1 @@
+((0_1888:0.0,1_1593:0.0,3_827:0.0):0.014969102,2_887:0.000000005,4_1812:0.063889720);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001573_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001573_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dac6919bc5bf6223d401abd0e11d10f1448ee8ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001573_tree_id.txt
@@ -0,0 +1 @@
+((1_1613:0.000000005,3_813:0.335423522)0.906:0.007608773,4_1835:0.023655341,(2_871:0.022920210,0_1908:0.025424145)0.612:0.007164103);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001574_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001574_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a41a437d8a2e88b67ace445f2bb39eaedf97e414
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001574_tree_id.txt
@@ -0,0 +1 @@
+(1_1614:0.005400293,4_1836:0.005428903,(0_1909:0.011174185,(2_870:0.034342639,3_812:0.532050021)0.857:0.027962343)0.882:0.007804605);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001575_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001575_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99ae28d4314c691e0e2790c9eb2f24b99c19877a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001575_tree_id.txt
@@ -0,0 +1 @@
+(0_1910:0.001342358,4_1837:0.006161978,(1_1615:0.009131694,(2_869:0.009186807,3_811:0.340357050)0.896:0.009062616)0.871:0.003032551);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001577_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001577_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..748991ac005b1333ed9388d7626ab6c59f591399
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001577_tree_id.txt
@@ -0,0 +1 @@
+(0_1912:0.006957727,(1_1617:0.0,4_1839:0.0):0.003523548,(2_867:0.043335116,3_809:0.331960902)0.959:0.034575114);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001579_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001579_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..237cb9d6d158aec77080527a00ef579a5a774900
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001579_tree_id.txt
@@ -0,0 +1 @@
+(0_1917:0.008171824,(1_1622:0.0,3_797:0.0):0.000000005,(2_861:0.341480523,4_1844:0.004080248)0.449:0.000000514);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001582_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001582_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da7d6e7df5d241a88ecd8a1559d6d32d828e2d23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001582_tree_id.txt
@@ -0,0 +1 @@
+(1_1625:0.001778633,4_1847:0.000000005,(3_794:0.007135030,(2_858:0.342411990,0_1920:0.000000006)0.485:0.001772571)0.792:0.001781983);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001587_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001587_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1313fee044810151fe65e9d2eb6cee5f37fda510
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001587_tree_id.txt
@@ -0,0 +1 @@
+(0_1928:0.018099132,(2_849:0.198244599,3_787:0.864734191)0.998:0.282662706,(4_1855:0.035892113,1_1633:0.021282696)0.779:0.014993185);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001589_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001589_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78c4f765e6fff582d7fc3c37da26da36ddd59ce2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001589_tree_id.txt
@@ -0,0 +1 @@
+(0_1930:0.013073648,1_1635:0.003671977,(4_1857:0.009393945,(2_847:0.019627492,3_786:0.016970114)0.959:0.068164913)0.745:0.001794185);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001590_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001590_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be8bf1af00b95ee05dbdf1f8c16375ab3140c532
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001590_tree_id.txt
@@ -0,0 +1 @@
+(0_1931:0.008255086,1_1636:0.008218864,(4_1858:0.006082016,(2_846:0.029820416,3_785:0.012317554)0.933:0.015250168)0.753:0.003561452);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001592_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001592_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ac0629c16d588f029cb2c72496a8058fe449d7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001592_tree_id.txt
@@ -0,0 +1 @@
+(0_1933:0.007871406,4_1860:0.002591255,(1_1638:0.000000005,(2_844:0.106952978,3_783:0.019518003)0.996:0.045481660)0.820:0.002611096);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001593_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001593_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0fff140addaec2a9ef763f2a00b6fc92f9591ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001593_tree_id.txt
@@ -0,0 +1 @@
+(0_1934:0.005153842,(2_841:0.022551873,3_780:0.032904743)1.000:0.216665642,(1_1639:0.011457087,4_1861:0.000000005)0.747:0.006336925);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001595_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001595_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3379510250a903f9675d7a15c105e9ccb21ea56d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001595_tree_id.txt
@@ -0,0 +1 @@
+(0_1938:0.020307766,(1_1643:0.0,4_1865:0.0):0.007260065,(2_839:0.112835502,3_776:0.360049427)0.999:0.101729534);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001598_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001598_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e52842cc96a45fc41979129a5616ec7f285a7d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001598_tree_id.txt
@@ -0,0 +1 @@
+(1_1664:0.004083565,4_1882:0.008244628,(0_1943:0.000000005,(2_819:0.071004039,3_757:0.415433899)0.990:0.110007546)0.689:0.008249610);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001599_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001599_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24ee465a71b5a6921f7b2561d87d105ee98e855c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001599_tree_id.txt
@@ -0,0 +1 @@
+(1_1666:0.021287290,4_1884:0.022145221,(0_1945:0.038774529,(2_817:0.242330448,3_755:1.136202757)0.991:0.219774644)0.801:0.012210352);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001606_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001606_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..26800d5b95556b55210e98fa4772a997a6c380ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001606_tree_id.txt
@@ -0,0 +1 @@
+(0_1952:0.004039465,(1_1673:0.0,4_1891:0.0):0.003562868,(2_810:0.075493077,3_748:0.120500489)0.991:0.071377324);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001607_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001607_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0f3be3b06834df2d5092273bf50b31ac2f6a464b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001607_tree_id.txt
@@ -0,0 +1 @@
+(2_787:0.039513888,4_1893:0.006087812,(1_1675:0.000000005,(0_1955:0.002374476,3_746:0.009627553)0.273:0.004795604)0.842:0.003690080);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001608_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001608_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..17dc79cad57d5e08c16a88431b36fd8615871c26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001608_tree_id.txt
@@ -0,0 +1 @@
+(3_745:0.016228736,2_786:0.022584252,(1_1676:0.010844121,(0_1956:0.015300182,4_1894:0.000000006)0.775:0.004640994)0.391:0.003784458);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001612_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001612_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..480e4c3033cf61d4276257f900f537d8fc63c525
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001612_tree_id.txt
@@ -0,0 +1 @@
+(2_779:0.386034997,1_1681:0.011281035,(0_1961:0.006607354,(3_740:0.018784368,4_1899:0.006578451)0.886:0.009378431)0.148:0.007527669);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001613_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001613_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7624e455cac17ac98a5b9307f682dbcf79dbcae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001613_tree_id.txt
@@ -0,0 +1 @@
+(0_1962:0.001730974,4_1900:0.005185847,(1_1682:0.006587721,(2_778:0.042957548,3_739:0.105194746)0.903:0.008091374)0.340:0.001392517);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001614_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001614_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b393313849d90aa1022e8e8653ec8c40830ab7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001614_tree_id.txt
@@ -0,0 +1 @@
+((2_777:0.000000005,3_2039:0.669221219)0.888:0.006583251,4_1901:0.000000005,(0_1963:0.016506739,1_1683:0.000000006)0.509:0.006568675);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001615_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001615_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b52de6f3697cd8647a91b43a3099d31667a27a94
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001615_tree_id.txt
@@ -0,0 +1 @@
+(0_1964:0.018232327,1_1684:0.017003242,(4_1902:0.014212450,(2_776:0.396829882,3_738:0.923967041)0.979:0.261382227)0.754:0.011543730);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001617_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001617_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..daf9daec5c981a3ef829575c17f624c6ecadfc5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001617_tree_id.txt
@@ -0,0 +1 @@
+(4_1904:0.002242601,1_1686:0.002235651,(0_1966:0.000000005,(2_774:0.020372879,3_735:0.022253982)0.874:0.005128611)0.817:0.002235746);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001620_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001620_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37c3b8dcfd7753090554eb850e7946992a782c5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001620_tree_id.txt
@@ -0,0 +1 @@
+(3_731:0.005818425,(0_1973:0.000000005,1_1691:0.000000005)0.906:0.005787432,(2_765:0.042969419,4_1909:0.004126429)0.748:0.002691503);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001621_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001621_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d8c98055bdb54e731a940b732143c0dcc980734
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001621_tree_id.txt
@@ -0,0 +1 @@
+((0_1974:0.0,1_1692:0.0):0.008187593,4_1910:0.012304824,(2_763:0.010730804,3_730:0.017111582)0.924:0.017666465);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001625_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001625_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3f423fe62cbbbf952f40f359d74e9279d9944d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001625_tree_id.txt
@@ -0,0 +1 @@
+(0_1991:0.000000005,1_1708:0.010936210,(4_1926:0.000000005,(2_752:0.121461395,3_722:0.180769159)0.997:0.180298855)0.811:0.005454977);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001626_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001626_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a021088cbb42b461c75cfe575754e4b5691b89bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001626_tree_id.txt
@@ -0,0 +1 @@
+(1_1709:0.012408485,4_1927:0.010801431,(0_1992:0.010868404,(2_751:0.071548742,3_116:0.313745562)1.000:0.074879765)0.742:0.005422938);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001627_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001627_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c71a832a6cf9a095d1e553d1e6e66ec65dfefb53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001627_tree_id.txt
@@ -0,0 +1 @@
+(1_1711:0.000000005,4_1929:0.000000005,(0_1994:0.006270779,(2_693:0.090316462,3_708:0.105962188)1.000:0.205656150)0.000:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001629_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001629_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8f39341b4625f6d66f88603eed1d1ce350306ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001629_tree_id.txt
@@ -0,0 +1 @@
+(0_1996:0.008502808,(2_745:0.109031534,3_709:0.158575808)0.998:0.100097516,(4_1931:0.021767939,1_1713:0.011087538)0.399:0.006638560);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001635_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001635_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8451a0f649791337b311b5aac320f136c57c67ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001635_tree_id.txt
@@ -0,0 +1 @@
+((0_2022:0.0,1_1738:0.0):0.000000005,4_1962:0.006305138,(2_682:0.012618043,3_593:0.012848562)0.917:0.019236695);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001637_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001637_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..101a9427d93e7e47bd639545a0c8162b1a09efa0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001637_tree_id.txt
@@ -0,0 +1 @@
+(2_680:0.011401453,4_1964:0.000000005,((0_2024:0.0,1_1740:0.0):0.008536598,3_591:0.005688178)0.774:0.002841241);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001639_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001639_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..334c018300eeb6e6eae870b77aa576ce4d2f837b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001639_tree_id.txt
@@ -0,0 +1 @@
+(3_589:0.006398404,4_1966:0.004634906,((0_2026:0.0,1_1742:0.0):0.002427151,2_678:0.013072286)0.811:0.004418201);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001640_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001640_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e911a45581edf57f3f109a40ec2c9425f7fa768
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001640_tree_id.txt
@@ -0,0 +1 @@
+((0_2027:0.0,1_1743:0.0):0.013764224,4_1967:0.009819106,(2_568:0.201311054,2_677:0.007104663)0.609:0.003089642);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001642_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001642_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..caba6d454bba69f53981963673d5059035c69f92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001642_tree_id.txt
@@ -0,0 +1 @@
+(3_581:0.020547210,2_665:0.043061928,(0_2034:0.032807564,(1_1753:0.034255208,4_1974:0.046064721)0.227:0.005594098)0.576:0.005872127);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001650_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001650_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ecd67cad0582f765cac959435a9fd385b55ae85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001650_tree_id.txt
@@ -0,0 +1 @@
+(4_1989:0.023931208,1_1766:0.014913762,(0_2048:0.005046415,(2_651:0.044997515,3_569:0.350474212)0.808:0.020056765)0.450:0.004903898);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001653_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001653_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad0d75f2c3e84755cd42ceb46c2df3f9b6ff3868
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001653_tree_id.txt
@@ -0,0 +1 @@
+(1_1772:0.057712723,4_1992:0.000000005,(0_2053:0.006033326,(2_648:0.094829837,3_565:0.352102478)0.991:0.134653097)0.728:0.021463882);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001655_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001655_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40474128a1b6f57372f84767d4c2939a27d17f25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001655_tree_id.txt
@@ -0,0 +1 @@
+((2_645:0.175044975,3_563:0.653149184)0.779:0.098164251,1_1775:0.010006758,(4_1995:0.010038507,0_2056:0.000000005)0.630:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001657_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001657_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b10bde8201b09a74b14ac57be518399ef4d02bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001657_tree_id.txt
@@ -0,0 +1 @@
+(0_2058:0.011344214,1_1777:0.000000005,(4_1997:0.013259764,(2_643:0.133787573,3_561:0.336956496)0.989:0.141374267)0.936:0.029963554);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001659_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001659_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fae7ebb0eace687bd50070c09af4ae272b44af48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001659_tree_id.txt
@@ -0,0 +1 @@
+(0_2060:0.021640551,2_641:0.063282360,((1_1779:0.0,4_1999:0.0):0.015726699,3_559:0.024226361)0.344:0.023054676);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001660_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001660_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a59d5837d6e25572149591bf091bc99e2b9d9b76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001660_tree_id.txt
@@ -0,0 +1 @@
+(3_557:0.000000005,2_638:0.111199940,((1_1781:0.0,4_2001:0.0):0.022457309,0_2062:0.015134665)0.432:0.007422697);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001661_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001661_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f86ae62625976cb8c00c963561f15bcc19a4d00
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001661_tree_id.txt
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+(0_2064:0.037828867,4_2003:0.009317408,(1_1783:0.009514770,(2_637:0.108140285,3_555:0.019667730)0.757:0.018597317)0.893:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001663_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001663_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e50f35db81e5e90dc6e9588d710b1ea9e827f5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001663_tree_id.txt
@@ -0,0 +1 @@
+(1_1785:0.010776718,2_635:0.026642586,(3_552:0.034087729,(0_2066:0.013363386,4_2005:0.010396191)0.965:0.017982612)0.453:0.003514985);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001664_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001664_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..377ea13930dd3501b67561982c42e19aa94b59e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001664_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001666_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001666_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d46069096746eb0af277aa6522c937e823b339b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001666_tree_id.txt
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+(3_549:0.022148151,(1_1788:0.006261649,4_2008:0.002124704)0.977:0.013212284,(0_2069:0.020045774,2_632:0.016879247)0.863:0.006068695);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001667_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001667_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0b300431c287799e1003b57b62aaaf7e7021ce0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001667_tree_id.txt
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+(2_631:0.007083817,(0_2070:0.000000005,1_1789:0.014084695)0.908:0.007021174,(3_548:0.035598207,4_2009:0.007122953)0.427:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001669_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001669_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6fe1233cdf969d946e84f14d1fa9ceb6aef5b14c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001669_tree_id.txt
@@ -0,0 +1 @@
+(0_2072:0.003598918,4_2011:0.001792335,(1_1791:0.005381411,(2_629:0.046534418,3_546:0.059771737)0.965:0.022718891)0.946:0.007256968);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001671_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001671_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e52b7f367572273d393373b5c8c059a8941cf9cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001671_tree_id.txt
@@ -0,0 +1 @@
+(0_2075:0.000000005,(1_1794:0.0,4_2014:0.0):0.014698718,(2_618:0.034877863,3_543:0.191921409)0.568:0.034406798);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001672_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001672_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe4e5e8533b908c239f58d85fa2bc837d8f9b748
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001672_tree_id.txt
@@ -0,0 +1 @@
+((0_2076:0.0,1_1795:0.0,4_2015:0.0):0.044124406,2_617:0.063107896,3_542:0.185200160);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001673_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001673_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..574e178f522832333469b29b7073bbf99f384134
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001673_tree_id.txt
@@ -0,0 +1 @@
+(0_2077:0.004338158,(1_1796:0.0,4_2016:0.0):0.002177444,(2_616:0.066884286,3_541:0.189921945)0.998:0.083167417);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001675_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001675_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20fbc896aa6b88472940a29e218b929e53f3d064
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001675_tree_id.txt
@@ -0,0 +1 @@
+(2_614:0.018387431,3_539:0.299388882,((0_2079:0.0,1_1798:0.0):0.000000005,4_2018:0.006990995)0.961:0.071370467);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001676_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001676_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..83e6ec2f3d1ded2144552f4ba356c898527f9fd2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001676_tree_id.txt
@@ -0,0 +1 @@
+(4_2019:0.009595917,(2_698:0.288232462,3_537:0.062564786)0.998:0.061046012,(0_2080:0.016527742,1_1799:0.007052546)0.352:0.006773108);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001678_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001678_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70a7dbb5bb3ca43e032e7ac43d8f0a233e940391
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001678_tree_id.txt
@@ -0,0 +1 @@
+(1_1801:0.000000005,4_2021:0.004285914,(3_535:0.013096992,(0_2083:0.024602531,2_610:0.009610263)1.000:0.117856791)0.896:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001679_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001679_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44e803476782a7b647b58bd61d9405f4439ed40a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001679_tree_id.txt
@@ -0,0 +1 @@
+(3_534:0.030032195,(1_1802:0.004900607,4_2022:0.000615738)1.000:0.099399988,(0_2084:0.037726343,2_609:0.034422192)1.000:0.081416729);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001683_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001683_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d285f186f519d5ae8894ffc4fadb95540347494
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001683_tree_id.txt
@@ -0,0 +1 @@
+(4_2032:0.000000006,(2_595:0.087706036,3_520:0.428518767)0.994:0.088706555,(0_2088:0.000000005,1_1812:0.002504645)0.980:0.011900982);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001686_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001686_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e8ddfff9627e872066891a42eb816c66df885ce
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001686_tree_id.txt
@@ -0,0 +1 @@
+((2_592:0.138389400,3_517:0.076287498)1.000:0.184286806,4_2035:0.012470923,(0_2091:0.022217427,1_1815:0.002452194)0.744:0.002332288);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001687_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001687_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e88c03d09d567770b1cc594d55de4dcfd67449ba
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001687_tree_id.txt
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+(0_2093:0.008841522,4_2037:0.002652646,(1_1817:0.003558783,(2_591:0.046924393,3_516:0.137503086)1.000:0.036622752)0.646:0.001777800);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001689_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001689_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b9fb9b0b4020de2ed90e2a5fdb61e8d82046af7
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001691_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001691_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a53e90fd0988ce5d87a63df51f9ed6cf3aac84e
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001694_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001694_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..59d350fa8c4f5d78962e8df358cc62a33085e402
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001698_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001698_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3dc6a965cf065f317ac4260e9b185311d910489
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+(0_2114:0.008064036,4_2060:0.000000005,(1_1839:0.002685601,(2_559:0.197606825,3_487:0.122682165)1.000:0.121589497)0.491:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001699_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001699_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75545cc994dbb580b89bd1f8120ffc2382cb42d5
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+(1_1840:0.002853160,4_2061:0.000000005,(0_2115:0.008144335,(2_558:0.336952356,3_486:0.194380345)0.999:0.159479730)0.597:0.000540501);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001700_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001700_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c67b9a0864b28867d16462c65bfaaf9a3db3a06e
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001701_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001701_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7fd9c7c1960e711691d8b735d621193bab12173
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001701_tree_id.txt
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+(4_2063:0.010106937,1_1842:0.000000005,(0_2117:0.000000005,(2_556:0.250565094,3_484:0.075571667)1.000:0.122480197)0.857:0.003354210);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001702_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001702_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..33d63620b3b8d9d3ee290ff0d36afd896b363499
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001706_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001706_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c81a179edd70fb166bd57b3bf7b2d3c732d440b0
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@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001708_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001708_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0cac59629e1f9b0899a9e5ebc44a57d3edee445
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001709_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001709_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7aa6c335d0f97546a7d7dbffc2220f151f13a9f2
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001718_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001718_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c11320e41450536f49f5fbc6978245ecfb06740b
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001719_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001719_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f052002ba138d9528b7b71e80d4251e952994040
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001719_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001720_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001720_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..60169f8194f2ae97dfa2094f0d2a42d13f646c78
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001721_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001721_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aad84e3d37ede75192d537e4b3f2acf7201a0102
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+(0_2155:0.007391169,1_1879:0.007353510,(4_2095:0.000000005,(2_507:0.109405722,3_450:0.322153187)0.999:0.146806853)0.978:0.026062909);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001722_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001722_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..07ecfaf6569043dd84ead5005d280ee146704dc8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001722_tree_id.txt
@@ -0,0 +1 @@
+((2_509:0.343557680,3_448:0.440091394)1.000:0.321391933,4_2098:0.004390187,(1_1882:0.026896576,0_2158:0.000000005)0.750:0.004474007);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001723_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001723_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b02094b3a2051ad35da6a35e225fa830a4d3fcb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001723_tree_id.txt
@@ -0,0 +1 @@
+(1_1883:0.010900106,4_2099:0.010726934,(0_2159:0.010770889,(2_497:0.128501258,3_445:0.128637325)1.000:0.316337794)0.850:0.011697987);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001726_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001726_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b8b22bf45397a98b030624e0596fa59288d756ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001726_tree_id.txt
@@ -0,0 +1 @@
+(0_2180:0.001703057,1_1893:0.001703579,(4_2113:0.001708457,(2_697:0.208089259,4_2153:0.325721445)1.000:0.398826573)0.830:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001728_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001728_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5654d2822ce3c752306b6bc5cd8cafb290fe0dae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001728_tree_id.txt
@@ -0,0 +1 @@
+((0_2184:0.0,1_1897:0.0,4_2117:0.0):0.076656806,2_482:0.097193281,3_494:0.693067531);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001729_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001729_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d7d6310380c7a3dc666c177624bb73bf1acc3e43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001729_tree_id.txt
@@ -0,0 +1 @@
+((1_1899:0.032752502,2_481:0.150596248)0.962:0.022239106,4_2119:0.005864006,(3_420:0.018140801,0_2186:0.000000006)0.517:0.003989559);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001730_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001730_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..61c1b920d0955ed110c5db833417360b7289f5e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001730_tree_id.txt
@@ -0,0 +1 @@
+(1_1904:0.015887733,4_2125:0.003978535,(2_459:0.024234957,(0_2193:0.001499587,3_415:0.080084704)0.720:0.002500502)0.828:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001732_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001732_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..29bfcc96726fa093608c9f73dd108348efb9a750
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001732_tree_id.txt
@@ -0,0 +1 @@
+((0_2195:0.0,1_1906:0.0,4_2127:0.0):0.009674446,2_457:0.026442625,3_413:0.025996207);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001733_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001733_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a804bd7235bc3eda19386d24c4b3466af1982e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001733_tree_id.txt
@@ -0,0 +1 @@
+((0_2196:0.0,1_1907:0.0,4_2128:0.0):0.010221499,2_456:0.031746844,3_412:0.040123522);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001735_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001735_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d966014e3dba0ea1e982c40dd4cea6fbb840040
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001735_tree_id.txt
@@ -0,0 +1 @@
+(0_2209:0.007650321,1_1913:0.001903079,(4_2142:0.000000006,(2_443:0.006627328,3_477:0.300678395)0.922:0.010622102)0.271:0.001907374);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001738_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001738_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d897a7f7ede30db7245b0472f4aee58154fae552
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001738_tree_id.txt
@@ -0,0 +1 @@
+(0_2225:0.005538028,4_2165:0.005545891,(1_1927:0.000000005,(2_433:0.027305128,3_387:0.208306068)0.756:0.006925595)0.000:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001740_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001740_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd3736be2e25e2c507e9b4e9e167feb9ab307b2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001740_tree_id.txt
@@ -0,0 +1 @@
+(2_431:0.041690776,3_384:0.159727993,(0_2228:0.006228182,(1_1931:0.0,4_2169:0.0):0.000000005)0.853:0.024614987);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001741_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001741_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f9042d6df2812a692d7aae32057816804760942
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001741_tree_id.txt
@@ -0,0 +1 @@
+((0_2229:0.0,1_1932:0.0,2_430:0.0,4_2170:0.0):0.006212319,3_383:0.006212319);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001742_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001742_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91ad7206a8777232631fec3a4dbc418a844e6c4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001742_tree_id.txt
@@ -0,0 +1 @@
+(1_1933:0.000000005,4_2171:0.005313600,(0_2230:0.005296771,(2_429:0.005562261,3_382:0.130381455)0.845:0.010397925)0.394:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001743_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001743_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a066b4d6386096fb395732a33670d2fba7d3da10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001743_tree_id.txt
@@ -0,0 +1 @@
+((0_2231:0.0,1_1934:0.0,4_2172:0.0):0.019909704,2_428:0.009138884,3_381:0.050481508);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001745_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001745_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f5efee71a14e791fde2b89f3cc3a6d5af75d675
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001745_tree_id.txt
@@ -0,0 +1 @@
+(0_2233:0.008520803,4_2175:0.008448284,(1_1937:0.020772640,(2_424:0.182841898,3_378:0.454984866)0.956:0.192174916)0.752:0.014245133);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001748_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001748_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb13a1eedb1465e2c1d3ac734ddc68a7ad805f00
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001748_tree_id.txt
@@ -0,0 +1 @@
+(0_2238:0.002088218,4_2180:0.000000005,(1_1942:0.010512606,(2_419:0.037565168,3_373:0.117388359)0.992:0.036937051)0.902:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001749_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001749_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24c01952fb33f682e0d9690c55f7d16ad0a62ff2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001749_tree_id.txt
@@ -0,0 +1 @@
+(0_2240:0.000000005,1_1944:0.001664767,(4_2182:0.005045601,(2_418:0.040947922,3_371:0.329159397)0.996:0.048465396)0.886:0.005126081);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001751_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001751_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62e2b8764a6e470b8cea624d4b8791caa74389ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001751_tree_id.txt
@@ -0,0 +1 @@
+((0_2243:0.0,1_1947:0.0,4_2185:0.0):0.060113395,2_415:0.017723551,3_368:0.130158233);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001753_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001753_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f3865322730f2be624c8503cf9530bcbca5ca3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001753_tree_id.txt
@@ -0,0 +1 @@
+(0_2246:0.008478396,4_2188:0.000000006,(1_1950:0.000000005,(2_411:0.041257293,3_365:0.261418777)0.924:0.034826117)0.814:0.004227734);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001758_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001758_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..621808dd170a804a688a2dc8de6261ba898f33d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001758_tree_id.txt
@@ -0,0 +1 @@
+((0_2251:0.0,1_1955:0.0,4_2193:0.0):0.022032407,2_406:0.021708701,3_360:0.021423098);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001759_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001759_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81eabed8ca2ec4d728bb3e24f061a17840bfec61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001759_tree_id.txt
@@ -0,0 +1 @@
+(1_223:0.433643656,2_2379:0.520145057,(1_193:0.939218750,(3_2262:0.392586173,4_493:0.180160029)1.000:0.707665518)0.956:0.258485635);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001761_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001761_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bfabc55b553ca7c029918db48d970e1e870f7caf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001761_tree_id.txt
@@ -0,0 +1 @@
+((1_313:0.0,1_352:0.0,1_1917:0.0,1_1965:0.0):0.117209965,1_1071:0.117209965);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001764_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001764_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e453b2471205401f3a143d6e3377baed6226e9f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001764_tree_id.txt
@@ -0,0 +1 @@
+((1_2079:0.0,4_120:0.0):0.018460533,2_254:0.022480653,(2_81:0.595089781,3_125:0.579158878)1.000:0.903728907);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001765_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001765_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8bf93882d0af2546640f7c8de748c964dd7ed66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001765_tree_id.txt
@@ -0,0 +1 @@
+((1_2080:0.0,4_121:0.0):0.000000005,2_253:0.040917231,(2_80:0.684780101,3_126:0.556352258)1.000:0.782349563);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001766_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001766_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b4c851cf5b36b5111152acf71e22a8368296ecc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001766_tree_id.txt
@@ -0,0 +1 @@
+((1_2154:0.0,4_210:0.0):0.021500154,2_510:1.181290662,(2_496:0.124228747,3_438:0.074010466)0.940:0.198477812);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001770_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001770_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10c05ce4840437a18a88e2eab1ba64edc053e62f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001770_tree_id.txt
@@ -0,0 +1 @@
+((0_9:0.0,1_1978:0.0):0.008032380,2_368:0.283530791,4_9:0.032509532);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001772_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001772_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..51ae9aa53cbe877239fb2c14f31cf9a70cce6cc0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001772_tree_id.txt
@@ -0,0 +1 @@
+(0_44:0.012288579,3_282:0.180366092,(1_2008:0.000000005,4_39:0.002004821)0.450:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001773_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001773_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a10ba4d8449d50b3a080852ae9b5a24e4623c51a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001773_tree_id.txt
@@ -0,0 +1 @@
+(1_2011:0.002291697,2_337:0.178153952,(0_47:0.017149386,4_42:0.004200706)0.740:0.008467633);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001774_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001774_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d82aced30d75af9d54dbe31f29289815d8dc657
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001774_tree_id.txt
@@ -0,0 +1 @@
+(0_48:0.012684538,2_336:0.108149318,(1_2012:0.000000005,4_43:0.006297949)0.761:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001775_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001775_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0cb38c6051961b65473cd607b3f054c22c83a1cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001775_tree_id.txt
@@ -0,0 +1 @@
+(1_2019:0.010704699,4_50:0.016264424,(0_55:0.000000005,2_321:0.428570578)0.762:0.005373793);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001779_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001779_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e2ce7aff7626fb088ed57dd4d3f97234b55157b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001779_tree_id.txt
@@ -0,0 +1 @@
+(0_113:0.022115616,(1_2077:0.0,4_118:0.0):0.004701807,3_187:0.298457282);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001781_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001781_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6802ae288ebdda7971e81cc3a203e6c41d3c68c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001781_tree_id.txt
@@ -0,0 +1 @@
+(0_124:0.000000005,(1_2089:0.0,4_132:0.0):0.011393515,2_243:0.298351519);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001783_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001783_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54132cdbd5e6ec4d38ccda217d1e1aa05c5b0209
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001783_tree_id.txt
@@ -0,0 +1 @@
+(1_2110:0.002076498,2_220:0.281316041,(0_145:0.002518855,4_153:0.008277566)0.747:0.006017510);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001785_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001785_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..960c5610449c04844c01c997b30afbd52d6ee4a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001785_tree_id.txt
@@ -0,0 +1 @@
+(0_169:0.009984017,1_2113:0.007242706,(2_215:0.147955099,4_161:0.039035198)0.966:0.035663065);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001787_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001787_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..04730a28c038e2692c755e05a5161bbe94c36a05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001787_tree_id.txt
@@ -0,0 +1 @@
+(0_192:0.277480393,2_179:0.240165584,(3_115:1.476603584,3_135:0.168787116)0.919:0.151148223);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001793_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001793_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca136395a9ddde1fa137347b4412fe8e798f5011
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001793_tree_id.txt
@@ -0,0 +1 @@
+(0_238:0.010797706,4_238:0.007131982,(1_2201:0.006100833,3_82:0.198053416)0.852:0.007283192);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001794_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001794_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c89831bae250297a290ee79013b40b484d8a27d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001794_tree_id.txt
@@ -0,0 +1 @@
+(2_109:0.029288522,4_243:0.004082465,(0_243:0.004280274,1_2206:0.001432344)0.249:0.002765966);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001799_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001799_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96d3a049a320d7f54433c7d0549f6eaf1c2e260c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001799_tree_id.txt
@@ -0,0 +1 @@
+(3_39:0.384951208,4_282:0.012113927,(0_276:0.030168115,1_2249:0.004022062)0.800:0.010457489);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001800_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001800_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aadd4b53ea2a78fb5dadc5d4978a02f61bb75689
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001800_tree_id.txt
@@ -0,0 +1 @@
+(0_277:0.030607338,2_59:0.147781845,(1_2250:0.005524592,4_283:0.018238794)0.411:0.012382981);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001801_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001801_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f4149bae9780753ed48568ee5322941a28da0fcd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001801_tree_id.txt
@@ -0,0 +1 @@
+(0_291:0.027103694,2_45:0.289748260,(1_8:0.004871657,4_298:0.012238987)0.938:0.021538579);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001804_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001804_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..180383f16bf7d6b291dfe708d7ed60f24b8527df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001804_tree_id.txt
@@ -0,0 +1 @@
+(0_315:0.000000005,(1_40:0.0,4_322:0.0):0.003708123,2_2:0.053776276);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001807_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001807_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1689ffb73f77d65158185a1135b64cca8dd4ac74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001807_tree_id.txt
@@ -0,0 +1 @@
+(1_99:0.028559419,3_2385:0.002953797,(0_366:0.004845313,4_372:0.024567636)0.385:0.009871786);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001815_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001815_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..85f29c837b74f98d45cf7e340f695880e8512fb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001815_tree_id.txt
@@ -0,0 +1 @@
+(0_513:0.000000006,(1_246:0.0,4_516:0.0):0.000000005,2_2360:0.166291382);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001818_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001818_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff6cfe4bdd2fb3ddbe9bffc830100f167d6ef47f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001818_tree_id.txt
@@ -0,0 +1 @@
+((0_553:0.0,1_294:0.0):0.000000005,2_2304:0.003862065,4_554:0.001930561);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001821_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001821_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8aeff7967372644ad0cda2f87eb016b3fa23fc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001821_tree_id.txt
@@ -0,0 +1 @@
+(0_599:0.009595659,(0_613:0.0,4_568:0.0):0.012363559,2_734:0.498122017);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001822_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001822_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ca73d4cf398563d643758b7ba735b05a893a5f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001822_tree_id.txt
@@ -0,0 +1 @@
+(0_600:0.083353335,2_731:0.024030650,(2_716:0.000000005,2_728:0.000000006)0.988:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001823_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001823_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f287d48fa8f0cb654e9fc2c45964fbb6123697fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001823_tree_id.txt
@@ -0,0 +1 @@
+(2_384:0.005831689,4_578:0.005785267,(0_603:0.003857454,3_2149:0.000000005)0.217:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001825_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001825_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65076165e810312ef80e5be4b1aecd030f9f1173
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001825_tree_id.txt
@@ -0,0 +1 @@
+((0_607:0.0,4_574:0.0):0.004310624,(2_388:0.0,3_2145:0.0):0.004310624);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001826_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001826_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4529e005cee3319520cd040d61f53f5158f5c835
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001826_tree_id.txt
@@ -0,0 +1 @@
+(0_610:0.008223319,3_2142:0.005476227,(4_571:0.002733691,2_391:0.000000005)0.629:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001828_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001828_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75e9d57848a7346d91f25e0421a0020c656721fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001828_tree_id.txt
@@ -0,0 +1 @@
+(1_361:0.009594895,3_2133:0.019250857,(0_615:0.270213826,4_584:0.025064070)0.668:0.004639755);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001829_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001829_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb6f265463e9029cf5e690d607f9eef81373c9ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001829_tree_id.txt
@@ -0,0 +1 @@
+(2_2266:0.279495914,4_591:0.000000005,(0_621:0.004878729,1_367:0.000000005)0.856:0.004873280);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001830_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001830_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a3e9f4bc41bd5303c5581347eeff019648cd14f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001830_tree_id.txt
@@ -0,0 +1 @@
+(0_637:0.001850225,(1_383:0.0,4_607:0.0):0.001850143,2_2250:0.047940826);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001832_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001832_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ec6c6e5cd35c608056f942d29969882cde3b4e6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001832_tree_id.txt
@@ -0,0 +1 @@
+((0_640:0.0,1_386:0.0):0.005583454,2_2246:0.120932551,4_610:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001833_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001833_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15b8f7cf83a2b416e744d7cd0aa0ed824d672d53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001833_tree_id.txt
@@ -0,0 +1 @@
+(0_641:0.016877679,2_2245:0.129649004,(1_387:0.006633318,4_611:0.009950139)0.805:0.006459512);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001836_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001836_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..60492daaadfd40d81348c3f378587694e75b33d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001836_tree_id.txt
@@ -0,0 +1 @@
+(1_453:0.028010718,4_677:0.049493012,(0_713:0.017080223,2_2141:0.399680934)0.867:0.024751501);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001839_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001839_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..173e9191f31eab9c319d49225e82de93adc9f73f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001839_tree_id.txt
@@ -0,0 +1 @@
+(3_1927:0.242943222,4_784:0.004018777,(1_556:0.009734423,0_825:0.005601251)0.393:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001840_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001840_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..982ad68bbc901d757c23424d3ffe4db197b46212
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001840_tree_id.txt
@@ -0,0 +1 @@
+(0_912:0.005461066,1_640:0.007681102,(1_1070:0.913524359,2_1949:0.052755002)0.998:0.102430602);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001847_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001847_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96a33180c33c180eb18b93d8bf65f5279e4ee7f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001847_tree_id.txt
@@ -0,0 +1 @@
+(1_750:0.000000005,3_2177:0.052159046,(0_1022:0.010200555,4_969:0.000000005)0.864:0.010230492);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001849_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001849_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b18ad00edd0e52dd2da841ca3a5c87e0740d7081
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001849_tree_id.txt
@@ -0,0 +1 @@
+((0_1032:0.0,1_760:0.0,4_981:0.0):0.205740397,2_2272:0.205740397);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001850_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001850_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca19ed97fad528bd347358cd4b3b0412922eeae7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001850_tree_id.txt
@@ -0,0 +1 @@
+(4_1015:0.015378925,1_793:0.003680845,(3_1642:0.206536336,0_1065:0.000000005)0.644:0.007430563);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001851_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001851_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37ece682300ef679ce7d2877aef2705006faabac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001851_tree_id.txt
@@ -0,0 +1 @@
+(1_794:0.000000005,2_1750:0.088588279,(0_1066:0.000000005,4_1016:0.002396687)0.996:0.012083238);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001852_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001852_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4976804d07b75c54fb18dcef0ddd5cc9c8b0c441
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001852_tree_id.txt
@@ -0,0 +1 @@
+(0_1099:0.017950277,(1_827:0.0,4_1049:0.0):0.045157356,3_1609:0.476342897);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001859_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001859_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6d0fef040bbc3c276ec9df2561347ba28671c6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001859_tree_id.txt
@@ -0,0 +1 @@
+((0_1258:0.0,1_990:0.0):0.000000005,3_1452:0.557374425,4_1215:0.014405704);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001861_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001861_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3f44d221a2cb80297a35f187e117bffa534ef0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001861_tree_id.txt
@@ -0,0 +1 @@
+((0_1309:0.0,4_1263:0.0):0.005982971,1_1038:0.005047430,3_1401:0.222008491);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001862_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001862_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..692eb8636373a57964606ad6c5ebfc139986e9fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001862_tree_id.txt
@@ -0,0 +1 @@
+((0_1334:0.0,4_1288:0.0):0.008603214,1_1063:0.014475477,3_1850:0.533158298);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001863_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001863_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6b02b8dc8e953a5d8d14ef46c0a48b0cdc3a11e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001863_tree_id.txt
@@ -0,0 +1 @@
+(0_1356:0.000000005,(1_1095:0.0,4_1305:0.0):0.003836810,3_1373:0.209856170);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001864_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001864_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..35d4fc929c413dce226f464ce0defb9f59671b12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001864_tree_id.txt
@@ -0,0 +1 @@
+(3_1368:0.154005250,4_1309:0.001826898,(0_1360:0.015023388,1_1099:0.004125763)0.529:0.002488187);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001865_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001865_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ec5a4b07cd637cc4975239d8cc2a8d7ad017978
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001865_tree_id.txt
@@ -0,0 +1 @@
+(4_1310:0.137590538,3_1367:0.616035099,(1_1100:0.002274145,0_1361:0.018194984)0.703:0.007634988);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001866_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001866_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b71082c2e72831b063298fc91d58eec2cbaa544
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001866_tree_id.txt
@@ -0,0 +1 @@
+(1_1101:0.000000005,3_1366:0.431462449,(0_1362:0.004233979,4_1311:0.000000005)0.863:0.020057788);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001868_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001868_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d23baf59782d7956be589658574a5f6d3c94a9b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001868_tree_id.txt
@@ -0,0 +1 @@
+(0_1393:0.015429262,4_1342:0.023343306,(1_1134:0.016603370,3_1332:0.682691702)0.767:0.015458193);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001873_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001873_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8636aa41248af9aa0aa522ac266daef2bb7b46a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001873_tree_id.txt
@@ -0,0 +1 @@
+(0_1453:0.011365351,3_623:0.285429624,(3_1709:0.0,3_2184:0.0):0.045235943);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001875_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001875_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e0188cb0c13f72f8a13175985025bfb51e29874
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001875_tree_id.txt
@@ -0,0 +1 @@
+(0_1529:0.002954222,1_1250:0.024068809,(2_1314:0.008929093,4_1456:0.002967685)0.779:0.002992016);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001876_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001876_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c88d4f6307b2eeb5208b78860f3dbcd743a5c8b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001876_tree_id.txt
@@ -0,0 +1 @@
+((0_1532:0.0,1_1253:0.0,4_1459:0.0):0.007244899,2_1311:0.007244899);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001879_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001879_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68ac5c28c9e8a72b5393f55058ede2431b84ec65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001879_tree_id.txt
@@ -0,0 +1 @@
+(2_1260:0.016194793,3_1165:0.010855906,(0_1560:0.010716592,1_1280:0.005358440)0.748:0.005247548);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001880_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001880_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ad59fe3ce0948e5f2e0d99d8939e17a0f84f6c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001880_tree_id.txt
@@ -0,0 +1 @@
+(0_1571:0.006101486,2_799:1.404624960,(1_1287:0.034543673,4_1500:0.014337127)0.750:0.008248821);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001881_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001881_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e892b47fb109d23546bbe8f1e42038382415c78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001881_tree_id.txt
@@ -0,0 +1 @@
+(1_1316:0.000000005,4_1531:0.009165818,(0_1601:0.000000005,4_1498:1.309372369)0.939:0.015356123);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001885_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001885_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66ae3a851a6ad2cb29cd3e9fc8a13875d2c1cd25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001885_tree_id.txt
@@ -0,0 +1 @@
+(0_1709:0.008406555,1_1426:0.001666476,(2_1089:0.205968075,4_1638:0.001457363)0.833:0.003564041);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001887_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001887_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc767902a73fc3fd7a4c281d551393c7ab07a9f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001887_tree_id.txt
@@ -0,0 +1 @@
+(0_1746:0.024955229,4_1668:0.000000005,(1_1454:0.025557306,3_984:0.184397958)0.857:0.010777700);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001888_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001888_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15aa7b7bea2ea1f5bc6c7692ca98a7d7ff893edf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001888_tree_id.txt
@@ -0,0 +1 @@
+(0_1777:0.015344427,(1_1485:0.0,4_1699:0.0):0.014712398,2_1011:0.259130497);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001889_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001889_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91ff195a202be297c36ad60e566a00533e05dd6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001889_tree_id.txt
@@ -0,0 +1 @@
+(2_1001:0.144081745,4_1708:0.006376612,(0_1787:0.003218260,1_1494:0.000000005)0.783:0.009753225);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001891_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001891_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..baf10b09e25b6565689d1571f20ed6329a282efd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001891_tree_id.txt
@@ -0,0 +1 @@
+(2_960:0.194885861,4_1740:0.016486173,(0_1819:0.007899566,1_1526:0.006366983)0.933:0.010114001);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001893_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001893_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..26444e5b5a5c3ae4ff017fd1d6fee687ae1977b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001893_tree_id.txt
@@ -0,0 +1 @@
+(0_1833:0.007749174,4_1754:0.003856770,(1_1540:0.010421327,2_945:0.079746832)0.484:0.005227680);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001896_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001896_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92da73271f38d3a50fdbf7bc01d9012340469073
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001896_tree_id.txt
@@ -0,0 +1 @@
+(4_1759:0.015715003,1_1545:0.005140712,(2_941:0.267932590,0_1838:0.013400446)0.187:0.007466751);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001897_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001897_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9515662a604763dce799682e31ca4ed0a60e71c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001897_tree_id.txt
@@ -0,0 +1 @@
+(1_1559:0.002014257,4_1773:0.002558375,(0_1852:0.009947070,3_864:0.126162126)0.888:0.011479226);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001900_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001900_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0d3663e97422404188bea7619f5348c97b2efb8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001900_tree_id.txt
@@ -0,0 +1 @@
+(4_1777:0.017051725,1_1563:0.001678088,(3_860:0.300900768,0_1856:0.004962739)0.553:0.003487282);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001902_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001902_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cdb0d02f09a415ac92ae61db21ebce0657f1a65c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001902_tree_id.txt
@@ -0,0 +1 @@
+(1_1578:0.003002981,2_909:0.146686422,(0_1871:0.006556803,4_1791:0.004111076)0.267:0.001918705);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001906_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001906_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..19dcc1a4afa19df67cd4aeee1ef85286f04b635c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001906_tree_id.txt
@@ -0,0 +1 @@
+(1_1620:0.023536251,4_1842:0.000000005,(0_1916:0.000000005,2_862:0.199906919)0.901:0.049136357);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001907_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001907_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d53ed5c2ad0aa429b1717b9fb36c1da946a4116b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001907_tree_id.txt
@@ -0,0 +1 @@
+((0_1926:0.0,1_1631:0.0,4_1853:0.0):0.003246593,2_851:0.003246593);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001909_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001909_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b83fccc53c8400517b67e3643e3efd6972a87b21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001909_tree_id.txt
@@ -0,0 +1 @@
+(1_1641:0.019543569,4_1863:0.019637375,(0_1936:0.006556715,3_778:1.010249361)0.705:0.013141372);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001911_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001911_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a709ea098b0e01e43afb791471f8d0929f0f8b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001911_tree_id.txt
@@ -0,0 +1 @@
+(1_1689:0.005206507,4_1907:0.008307654,(0_1971:0.006362684,2_770:0.012954848)0.347:0.001935754);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001914_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001914_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7dcb34da760b9ef585f65eecae20df7db1676127
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001914_tree_id.txt
@@ -0,0 +1 @@
+(1_1702:0.007522293,4_1920:0.017648369,(0_1985:0.005061548,3_716:0.007542448)0.761:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001916_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001916_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c821a32f75d7006ffdef489f1ffdffe310c7a38a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001916_tree_id.txt
@@ -0,0 +1 @@
+(0_1988:0.002442697,3_713:0.236510511,(1_1705:0.007268014,4_1923:0.000000005)0.164:0.004792905);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001917_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001917_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2afa0263923fb9b2b0580555d93aec2149aa5ef9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001917_tree_id.txt
@@ -0,0 +1 @@
+(1_1710:0.023295409,2_748:0.599072546,(0_1993:0.023817027,4_1928:0.082379630)0.876:0.072511003);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001918_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001918_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c6789fc927577b6bb8ba58466d17c375439f27d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001918_tree_id.txt
@@ -0,0 +1 @@
+(0_2001:0.000000005,3_2170:0.006235756,(3_2370:0.971759109,3_2384:1.624066803)0.915:0.323515928);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001921_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001921_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bbd818aa20b0cc8b64906ab9f2d391c0f8d8e6ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001921_tree_id.txt
@@ -0,0 +1 @@
+(1_1754:0.000000005,4_1977:0.002358402,(0_2036:0.023970985,2_664:0.196916163)0.940:0.019914862);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001923_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001923_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d4353bb796feaa800128d8ac630e30649633fc0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001923_tree_id.txt
@@ -0,0 +1 @@
+((0_2040:0.0,1_1758:0.0):0.010052008,2_660:0.408791908,4_1981:0.005224960);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001927_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001927_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..42a11001285904dba1e7e025bd0f17942b122f45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001927_tree_id.txt
@@ -0,0 +1 @@
+(0_2074:0.008949283,(1_1793:0.0,4_2013:0.0):0.011989695,2_619:0.015038901);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001932_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001932_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eeeb629c44ce2a2017e4e10cc582c0b3369f4e25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001932_tree_id.txt
@@ -0,0 +1 @@
+(1_1851:0.007653272,4_2072:0.003832294,(0_2126:0.008371173,2_544:0.409497495)0.184:0.024301041);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001933_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001933_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e25fbdeef788926d087907a6204a87544d434ec5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001933_tree_id.txt
@@ -0,0 +1 @@
+(1_1852:0.028851457,4_2073:0.009294938,(0_2127:0.040800864,2_543:0.087166629)0.830:0.023241305);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001934_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001934_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4ce7783bb207cba2e430899289d317f79695745
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001934_tree_id.txt
@@ -0,0 +1 @@
+(0_2131:0.017670284,4_2076:0.036147243,(1_1855:0.000000005,2_532:0.054399968)0.798:0.018026880);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001938_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001938_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20a21297393a4573c5d6de14b57a4137e3081c58
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001938_tree_id.txt
@@ -0,0 +1 @@
+((0_2148:0.0,1_1872:0.0):0.046867257,2_517:0.064669527,2_2586:1.702161039);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001942_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001942_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..007e9503807086bc9a7910236cf33bb55c800a15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001942_tree_id.txt
@@ -0,0 +1 @@
+(1_1887:0.005535797,2_498:0.381853786,(0_2160:0.020261934,4_2100:0.004984503)0.760:0.004596477);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001943_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001943_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8134543e7ada51f7738769ee45047d64f6423896
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001943_tree_id.txt
@@ -0,0 +1 @@
+(0_2161:0.000000005,3_444:0.132087846,(1_1888:0.011479568,4_2101:0.002283520)0.859:0.002286638);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001947_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001947_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1efcbad767966b99b32945af189a9c833f66c2db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001947_tree_id.txt
@@ -0,0 +1 @@
+(1_1914:0.028917495,3_393:0.438684755,(0_2211:0.078951212,2_442:0.031918602)0.344:0.038077440);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001948_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001948_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d1ec18d50ea9a26325082082acc36f87141d6f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001948_tree_id.txt
@@ -0,0 +1 @@
+(1_1915:0.015935516,2_441:0.018434322,(0_2212:0.032717618,3_391:0.060987213)0.864:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001950_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001950_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..955ef60a0685835e903ace93a3bca4ddaac473b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001950_tree_id.txt
@@ -0,0 +1 @@
+(2_435:0.032931346,4_2163:0.000000005,(0_2223:0.002469878,1_1925:0.000000005)0.951:0.004946584);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001951_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001951_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ecd151988ddfec80af532607659028f3bd1142de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001951_tree_id.txt
@@ -0,0 +1 @@
+(0_2237:0.016633945,4_2179:0.000000005,(1_1941:0.016241069,2_925:0.443059608)0.626:0.007221036);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001952_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001952_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e3d4f0b159d6956cc20ee810c82b5d3bce83b7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001952_tree_id.txt
@@ -0,0 +1 @@
+((0_2239:0.0,1_1943:0.0,4_2181:0.0):0.101546377,3_372:0.101546377);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001955_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001955_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8257a8fffdef15ba5db4eee181218a37f2f877c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001955_tree_id.txt
@@ -0,0 +1 @@
+(3_2246:0.089771232,4_511:0.032302137,(1_241:0.033837483,2_2365:0.879987394)0.516:0.038116977);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001956_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001956_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3a0660ab4637d5156212fefc56e2ac04015d10d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001956_tree_id.txt
@@ -0,0 +1 @@
+(1_243:0.004159527,4_513:0.009746539,(2_2363:0.181118016,3_2244:0.434029579)0.999:0.156571147);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001958_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001958_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ba995a28cc9178697cacca593d6abe73e8ea656f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001958_tree_id.txt
@@ -0,0 +1 @@
+(2_885:0.002808558,3_825:0.004380665,(1_1594:0.017932086,4_1814:0.342437850)0.899:0.012912212);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001959_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001959_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..605c6810e6a8f3b10a8b3023f3eaba8def161449
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001959_tree_id.txt
@@ -0,0 +1 @@
+(1_1595:0.008840655,4_1815:0.189836404,(2_884:0.001944200,3_824:0.000000005)0.998:0.035290580);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001960_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001960_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c363982e382b5d2d5daa433133e73ee1eb7b7fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001960_tree_id.txt
@@ -0,0 +1 @@
+(1_1596:0.003306949,(2_883:0.0,3_823:0.0):0.076933753,4_1816:0.006429566);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001961_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001961_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..adf55c3245f4c6dcee1e28900c415696866e5a6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001961_tree_id.txt
@@ -0,0 +1 @@
+(2_882:0.022694102,3_822:0.010021755,(1_1597:0.010155578,4_1817:0.011764372)0.697:0.003998458);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001964_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001964_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45802b9ac9e08c55221b8d2221cfcbe49a80c3f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001964_tree_id.txt
@@ -0,0 +1 @@
+(1_1648:0.070251706,2_834:0.036439532,(3_772:0.284694490,4_710:1.402463847)0.977:0.255956739);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001969_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001969_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a53eff2a32cf7dc47b6b7a2174a27ff36eafea8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001969_tree_id.txt
@@ -0,0 +1 @@
+(1_1656:0.000000005,4_1874:0.006825641,(2_827:0.134102420,3_761:0.078197546)0.944:0.047952376);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001970_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001970_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..add279415323c1b1d5055aaa74a8a3e10faca99e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001970_tree_id.txt
@@ -0,0 +1 @@
+((1_1657:0.0,4_1875:0.0):0.093891435,2_826:0.197823112,3_760:0.192042303);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001972_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001972_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d0479ffa085a1650c71470b154f09909d5d330fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001972_tree_id.txt
@@ -0,0 +1 @@
+((1_1736:0.0,4_1960:0.0):0.005008415,2_684:0.010265248,3_595:0.025747920);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001977_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001977_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2a151efde82fc89ce1d5236899510bf49f891bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001977_tree_id.txt
@@ -0,0 +1 @@
+(3_680:0.010670651,3_703:0.023305719,(2_694:0.277121640,3_404:0.269298374)0.992:0.248000946);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001978_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001978_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7a204abc0b6c82f6338f6667317f681c12ccec8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001978_tree_id.txt
@@ -0,0 +1 @@
+((2_715:0.0,2_732:0.0):0.065801231,2_2277:0.000000005,3_398:0.161675692);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001986_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001986_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47cbce534a1b0e7d9e0f9d89c53ca3fcae3b7885
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001986_tree_id.txt
@@ -0,0 +1 @@
+(0_10:0.000000006,1_1979:0.023492491,4_10:0.004628631);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001991_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001991_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7a172ab033cdae3919546b22084d560faec99ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001991_tree_id.txt
@@ -0,0 +1 @@
+(0_34:1.506596458,2_201:0.057177102,4_180:0.026955380);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001992_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001992_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4bf7dd91a015162e00da3e115cb09cfa099f4100
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001992_tree_id.txt
@@ -0,0 +1 @@
+(0_116:0.001576515,3_185:0.160387837,4_124:0.001224411);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001993_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001993_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..950403f110856c1cc638f57bd316d557ae7e4cc6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001993_tree_id.txt
@@ -0,0 +1 @@
+(0_158:0.000000005,1_337:0.003455369,1_1973:1.624504059);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001994_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001994_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..704548006e68826f45e54c4f75b52039478e496e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001994_tree_id.txt
@@ -0,0 +1 @@
+((0_159:0.0,0_2017:0.0):0.003394640,1_1731:0.003394640);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001996_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001996_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3fbb47687360ba8a14608e4a7b43822147d0f0c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001996_tree_id.txt
@@ -0,0 +1 @@
+(0_197:0.009456222,2_189:0.589414711,3_129:0.010671144);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001998_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001998_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..872b5225b5c7aeaf476a5dbff4747590973a9228
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001998_tree_id.txt
@@ -0,0 +1 @@
+(0_262:0.0,1_2228:0.0,4_260:0.0);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002000_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002000_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9a22a5ab07cb204597e44c355e1af7df15bc44a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002000_tree_id.txt
@@ -0,0 +1 @@
+((0_354:0.0,4_361:0.0):0.005754614,2_2531:0.005754614);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002005_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002005_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4bdb9781a285c97d8008605c6dbb491f7c3b2265
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002005_tree_id.txt
@@ -0,0 +1 @@
+(0_475:0.0,1_205:0.0,4_474:0.0);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002007_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002007_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2abe62ffec9226f7756a83757dd9a631b9b004ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002007_tree_id.txt
@@ -0,0 +1 @@
+(0_492:0.239542775,1_226:0.333599791,2_2383:0.325744136);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002008_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002008_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..59191aae4714a08d7c973b9b7692913f25084b5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002008_tree_id.txt
@@ -0,0 +1 @@
+(0_502:0.034896824,1_232:0.002256809,4_502:0.016653885);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002009_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002009_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9f738190b1cd37089894af25b5361cb38075210
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002009_tree_id.txt
@@ -0,0 +1 @@
+(0_505:0.059789056,1_235:0.000000005,4_505:0.031457419);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002010_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002010_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..039576ba0c3cc49807f10eed967d22d47bb39cf8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002010_tree_id.txt
@@ -0,0 +1 @@
+(0_558:0.071864057,1_300:0.000000005,4_559:0.011605997);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002012_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002012_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..afc143041f1892100e35eaaf40c9124d8334a203
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002012_tree_id.txt
@@ -0,0 +1 @@
+(0_575:0.463451774,3_1765:2.014300498,3_2189:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002015_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002015_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54215954557500efce198cc7d20f6be98f1e5f6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002015_tree_id.txt
@@ -0,0 +1 @@
+(0_676:0.598861610,(0_858:0.0,1_589:0.0):0.598861610);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002017_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002017_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7217edccca3387fd87a5d4ec837c69f330ea07d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002017_tree_id.txt
@@ -0,0 +1 @@
+(0_780:0.006476040,1_521:0.008511241,4_749:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002018_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002018_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b86ecb3d3a4909c9a576bd5a3f1ee3c8b00ce97a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002018_tree_id.txt
@@ -0,0 +1 @@
+((0_799:0.0,1_540:0.0):0.007780870,4_768:0.007780870);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002021_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002021_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f60f26014602d3aedeb88d9e0b327ff52daf7ee2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002021_tree_id.txt
@@ -0,0 +1 @@
+(0_910:0.014929247,1_638:0.025910812,2_1951:0.299805088);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002022_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002022_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f90893d675c95b6d1ed37b73c22c0ac27246190b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002022_tree_id.txt
@@ -0,0 +1 @@
+(0_911:0.012278519,1_639:0.026545895,2_1950:0.185795003);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002023_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002023_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..51dcc71a777c112826dbdbf64258096ebbf9cbfc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002023_tree_id.txt
@@ -0,0 +1 @@
+(0_914:0.739649813,2_1896:0.114656734,2_2053:0.331926630);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002025_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002025_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0f509c8553e5f841413bee77bf525448b0b642a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002025_tree_id.txt
@@ -0,0 +1 @@
+((0_997:0.0,1_719:0.0):0.006949362,4_939:0.006949362);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002027_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002027_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cdbfdf1ba18262fc7c7a8ff86b4c9e382df426b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002027_tree_id.txt
@@ -0,0 +1 @@
+(0_1243:0.000000005,1_971:0.006162301,4_1200:0.013982551);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002029_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002029_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cad8b679e0d0775026e339a3b40a3da3df086096
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002029_tree_id.txt
@@ -0,0 +1 @@
+((0_1266:0.0,2_1548:0.0):0.222976900,3_1444:0.222976900);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002030_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002030_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6fe8a31a8c38420c8782760b30533bf6b242068b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002030_tree_id.txt
@@ -0,0 +1 @@
+(0_1337:0.0,1_1074:0.0,4_1291:0.0);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002031_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002031_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8572846c91b28952a00beae3fd88ddc1942fa7f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002031_tree_id.txt
@@ -0,0 +1 @@
+(0_1342:0.0,1_1083:0.0,4_1292:0.0);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002034_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002034_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..32a6dec62a4b33d25a0c83474fe3fdcdc3af21f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002034_tree_id.txt
@@ -0,0 +1 @@
+(0_1348:0.0,1_1090:0.0,4_1297:0.0);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002035_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002035_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8557a819f7f4ef844a131fa76cb401bb1602cf3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002035_tree_id.txt
@@ -0,0 +1 @@
+(0_1454:0.022306889,(3_1710:0.0,3_2183:0.0):0.022306889);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002036_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002036_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..206e14c2747abcba35dd1cd195e7f9b3a65c41ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002036_tree_id.txt
@@ -0,0 +1 @@
+(0_1539:0.005438126,1_1261:0.018973156,4_1466:0.008012513);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002039_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002039_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16de590d1ce98ce7966acc19a8673f2057072c45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002039_tree_id.txt
@@ -0,0 +1 @@
+(0_1563:0.008455846,0_1978:1.971378110,2_1254:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002040_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002040_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5bc69aafc5a57721d7fb53c6d57b23eda82379c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002040_tree_id.txt
@@ -0,0 +1 @@
+(0_1564:0.018023399,2_1253:0.012782981,3_1161:0.020409963);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002043_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002043_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90bc72dcbfc1d31587f05926cf5973bd30ef927f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002043_tree_id.txt
@@ -0,0 +1 @@
+(0_1569:0.552912381,4_2143:0.490391345,4_2146:0.875927582);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002046_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002046_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f02902415f0e0f9d581039d766d8ebab996b2f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002046_tree_id.txt
@@ -0,0 +1 @@
+(0_1901:0.018390843,1_1605:0.010936609,4_1828:0.033547947);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002047_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002047_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bfc69009a93f4de48fa7225b2dea9677803afcdf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002047_tree_id.txt
@@ -0,0 +1 @@
+(0_1902:0.010337174,1_1606:0.010353636,4_1829:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002049_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002049_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..337a7b86d9c07a621356af63a289f02d480a973d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002049_tree_id.txt
@@ -0,0 +1 @@
+(0_1905:0.005044801,1_1608:0.000000005,4_1832:0.010112654);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002055_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002055_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..04dc9b120bc24339f1023f6bdc64708884fc55d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002055_tree_id.txt
@@ -0,0 +1 @@
+(0_2092:0.002608155,(1_1816:0.0,4_2036:0.0):0.002608155);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002056_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002056_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ceee033a4e2e47cc4d067dda616159ae9ac2003
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002056_tree_id.txt
@@ -0,0 +1 @@
+(0_2104:0.002966820,1_1829:0.000000005,4_2050:0.002966699);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002058_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002058_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..483cb3ac2cd3b7c21fd6cff65858fb18b3061b3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002058_tree_id.txt
@@ -0,0 +1 @@
+(0_2130:0.454496732,2_533:0.000000005,3_457:0.183757270);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002061_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002061_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..451c3272e8b657fc935cd5c3350774274e11e80a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002061_tree_id.txt
@@ -0,0 +1 @@
+((0_2144:0.0,4_2089:0.0):0.004446579,1_1868:0.004446579);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002065_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002065_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ffd01f31925fd3695064bee4e87038866aa9dcc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002065_tree_id.txt
@@ -0,0 +1 @@
+(0_2156:0.005774449,1_1880:0.036210812,4_2096:0.005873848);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002067_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002067_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0dc8a97aaec9d41bed4d39528aa472690ab4a626
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002067_tree_id.txt
@@ -0,0 +1 @@
+(0_2182:0.0,1_1895:0.0,4_2115:0.0);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002070_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002070_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf555a0590e9fce7a634cdbeaef4abe9284f2408
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002070_tree_id.txt
@@ -0,0 +1 @@
+((0_2203:0.0,1_1909:0.0):0.012316973,4_2135:0.012316973);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002071_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002071_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5899a8b69fde2ec50b7eaef7266c0b33eedc30b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002071_tree_id.txt
@@ -0,0 +1 @@
+(0_2206:0.000000005,2_450:0.028081788,4_2139:0.006930895);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002074_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002074_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a47bfad302d19a6cfbd0893d3f2c0be628609e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002074_tree_id.txt
@@ -0,0 +1 @@
+(1_89:0.706911330,(1_2241:0.0,4_274:0.0):0.706911330);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002075_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002075_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ccb6623319b5926a4bbc76cc1d94cb2bc274ad71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002075_tree_id.txt
@@ -0,0 +1 @@
+(1_221:0.793220116,2_2376:0.667129163,3_2259:0.471521136);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002076_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002076_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c4c647be7bc457866ebc8a840a605c76968d8fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002076_tree_id.txt
@@ -0,0 +1 @@
+(1_228:0.468002066,2_2377:0.325632311,4_491:0.387980720);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002077_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002077_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8e5cd114a17ce7a6422ce20b9c855e3ff08a112
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002077_tree_id.txt
@@ -0,0 +1 @@
+((1_308:0.0,2_2222:0.0):0.000000003,3_1787:0.000000003);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002079_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002079_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad78328ac394b243c210d5ec53e443d305a86e4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002079_tree_id.txt
@@ -0,0 +1 @@
+(1_342:0.035978504,(3_655:0.0,4_1952:0.0):0.035978504);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002081_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002081_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34a08f38ac4f46bc6711dd70f02ab3ec7d906983
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002081_tree_id.txt
@@ -0,0 +1 @@
+((1_354:0.0,3_2151:0.0):0.054160811,4_105:0.054160811);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002082_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002082_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1380b4328921705539e81eb90bd461d3c3d7a37e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002082_tree_id.txt
@@ -0,0 +1 @@
+(1_520:0.001479384,2_781:0.638211636,4_748:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002084_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002084_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62d3c30a0a132af970af2d897e1925bf74fdcb61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002084_tree_id.txt
@@ -0,0 +1 @@
+(1_1066:0.097363216,2_2594:0.222186010,3_1735:0.200774735);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002085_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002085_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ea9b4245652317742062ba07801ac6679c325cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002085_tree_id.txt
@@ -0,0 +1 @@
+(1_1080:0.010131044,1_1916:0.031756005,2_136:0.230068745);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002089_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002089_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..424d3bd7916162e6c83cc74e949d7ba346897436
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002089_tree_id.txt
@@ -0,0 +1 @@
+((1_1654:0.0,4_1872:0.0):0.154565433,3_765:0.154565433);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002090_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002090_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ddc4c3ac06c75c3c938da88cebb035e5cd24b394
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002090_tree_id.txt
@@ -0,0 +1 @@
+((1_1659:0.0,4_1877:0.0):0.132588048,2_824:0.132588048);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002094_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002094_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18abdb5ca819c4c980ac37c49ba53c7b314af2d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002094_tree_id.txt
@@ -0,0 +1 @@
+((1_1698:0.0,4_1916:0.0):0.838490210,2_2161:0.838490210);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002095_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002095_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4dc18c48b3182b9946b5199c15aa235112632e8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002095_tree_id.txt
@@ -0,0 +1 @@
+(1_1725:0.000000005,2_713:0.005630506,3_662:0.908836409);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002097_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002097_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d94f30220960bfd1c18632353f05ad9750786a9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002097_tree_id.txt
@@ -0,0 +1 @@
+(1_1745:0.017146500,2_675:0.001882755,2_792:1.377074511);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002102_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002102_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5a26076719f0ea5fbfce2a10f70be0c1dd13bf7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002102_tree_id.txt
@@ -0,0 +1 @@
+(1_2127:0.011909247,3_148:0.015126904,4_177:0.022153093);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002106_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002106_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca25ebc6fbe7db06b08f06179b90dc92b2b5ffa2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002106_tree_id.txt
@@ -0,0 +1 @@
+(2_552:0.343143429,3_480:0.376137159,3_642:1.480272929);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002108_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002108_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc9344e99652540ae28fbd8bd6b7ed0d093debf7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002108_tree_id.txt
@@ -0,0 +1 @@
+(2_743:0.208042917,3_706:0.198147675,4_1933:0.475577895);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002110_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002110_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c4adbf2bbf83d387b3336f79e358e6a7a4d75b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002110_tree_id.txt
@@ -0,0 +1 @@
+(2_878:0.000000005,2_1289:0.262778688,2_1291:0.430288174);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002112_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002112_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0271bc3fc5fe46b76f069e7fd65bfe7e5a97e031
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002112_tree_id.txt
@@ -0,0 +1 @@
+(2_1056:0.102179785,3_992:0.104530331,4_1660:0.332608447);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002115_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002115_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db58f361b105716cba1152ad6320c50d73803f80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002115_tree_id.txt
@@ -0,0 +1 @@
+(2_2278:0.154761250,3_332:0.905599912,3_676:0.095617630);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002116_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002116_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd35945ed65f8797dd40788fa5c0331a7005b017
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002116_tree_id.txt
@@ -0,0 +1 @@
+(2_2378:1.170356268,3_2223:0.885038410,3_2258:0.383494508);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002117_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002117_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e53e08122d117c25bcc925f5600397aa97546eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002117_tree_id.txt
@@ -0,0 +1 @@
+(3_315:0.137215559,3_399:0.092783424,3_648:0.069140261);