diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000002_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000002_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000003_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000003_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000004_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000004_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000010_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000010_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000015_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000015_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000019_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000019_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000020_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000020_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000021_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000021_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000024_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000024_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000025_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000025_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000026_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000026_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000031_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000031_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000034_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000034_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000035_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000035_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000036_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000036_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000038_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000038_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000039_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000039_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000048_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000048_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000050_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000050_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000051_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000051_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000058_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000058_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000062_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000062_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000063_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000063_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000066_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000066_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000069_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000069_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000070_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000070_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000071_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000071_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000083_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000083_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000085_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000085_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000086_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000086_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000090_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000090_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000094_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000094_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000116_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000116_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000118_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000118_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000120_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000120_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000122_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000122_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000126_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000126_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000127_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000127_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000130_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000130_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000137_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000137_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000141_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000141_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000143_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000143_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000149_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000149_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000174_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000174_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000178_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000178_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000181_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000181_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000191_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000191_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000192_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000192_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000201_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000201_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000205_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000205_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000207_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000207_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000210_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000210_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000212_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000212_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000213_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000213_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000218_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000218_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000230_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000230_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000234_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000234_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000236_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000236_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000237_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000237_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000240_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000240_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000244_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000244_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000245_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000245_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000246_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000246_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000248_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000248_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000253_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000253_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000256_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000256_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000257_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000257_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000262_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000262_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000264_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000264_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000267_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000267_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000268_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000268_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000269_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000269_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000271_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000271_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000278_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000278_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000279_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000279_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000280_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000280_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000281_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000281_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000286_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000286_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000288_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000288_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000289_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000289_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000292_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000292_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000299_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000299_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000306_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000306_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000307_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000307_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000308_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000308_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000309_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000309_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000316_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000316_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000340_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000340_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000345_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000345_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000370_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000370_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000374_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000374_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000572_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000572_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000574_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000574_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000576_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000576_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000578_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000578_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000580_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000580_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000587_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000587_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000588_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000588_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000589_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000589_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000596_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000596_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000599_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000599_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000606_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000606_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000796_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000796_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000805_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000805_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000813_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000813_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000840_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000840_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000843_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000843_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000844_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000844_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000846_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000846_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000847_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000847_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000848_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000848_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000852_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000852_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000853_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000853_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000854_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000854_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000855_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000855_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000856_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000856_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000857_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000857_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000859_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000859_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000861_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000861_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000863_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000863_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000874_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000874_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000881_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000881_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000887_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000887_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000940_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000940_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000974_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000974_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001014_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001014_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001017_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001017_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001021_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001021_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001023_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001023_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001025_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001025_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001026_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001026_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001031_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001031_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001032_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001032_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001033_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001033_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001038_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001038_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001040_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001040_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001043_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001043_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001044_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001044_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001045_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001045_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001050_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001050_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001051_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001051_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001052_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001052_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001055_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001055_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001058_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001058_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001060_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001060_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001061_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001061_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001064_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001064_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001065_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001065_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001066_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001066_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001085_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001085_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001112_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001112_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001113_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001113_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001115_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001115_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001132_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001132_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001135_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001135_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001156_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001156_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001158_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001158_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001159_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001159_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001160_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001160_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001161_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001161_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001162_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001162_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001163_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001163_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001164_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001164_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001165_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001165_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001170_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001170_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001171_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001171_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001173_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001173_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001175_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001175_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001177_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001177_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001178_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001178_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001180_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001180_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001181_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001181_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001182_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001182_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001185_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001185_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001189_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001189_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001190_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001190_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001197_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001197_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001199_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001199_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001201_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001201_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001203_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001203_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001204_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001204_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001206_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001206_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001207_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001207_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001208_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001208_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001213_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001213_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001216_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001216_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001217_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001217_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001219_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001219_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001220_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001220_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001222_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001222_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001223_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001223_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001224_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001224_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001229_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001229_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001230_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001230_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001235_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001235_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001236_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001236_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001237_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001237_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001238_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001238_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001239_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001239_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001242_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001242_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001244_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001244_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001247_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001247_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001248_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001248_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001251_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001251_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001255_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001255_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001256_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001256_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001258_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001258_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001259_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001259_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001260_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001260_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001262_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001262_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001263_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001263_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001264_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001264_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001267_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001267_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001269_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001269_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001270_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001270_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001274_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001274_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001276_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001276_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001277_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001277_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001279_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001279_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001282_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001282_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001286_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001286_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001288_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001288_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001289_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001289_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001290_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001290_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001299_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001299_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001300_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001300_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001301_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001301_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001303_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001303_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001304_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001304_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001305_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001305_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001308_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001308_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001310_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001310_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001315_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001315_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001318_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001318_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001324_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001324_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001335_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001335_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001336_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001336_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001338_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001338_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001339_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001339_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001340_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001340_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001341_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001341_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001342_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001342_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001344_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001344_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001350_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001350_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001351_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001351_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001354_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001354_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001356_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001356_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001359_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001359_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001365_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001365_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001366_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001366_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001376_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001376_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001377_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001377_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001378_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001378_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001379_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001379_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001383_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001383_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001384_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001384_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001386_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001386_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001391_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001391_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001393_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001393_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001395_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001395_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001396_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001396_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001399_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001399_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001400_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001400_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001401_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001401_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001402_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001402_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001405_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001405_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001409_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001409_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001410_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001410_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001419_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001419_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001420_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001420_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001422_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001422_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001423_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001423_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001424_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001424_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001425_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001425_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001430_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001430_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001432_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001432_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001435_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001435_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001440_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001440_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001441_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001441_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001444_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001444_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001461_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001461_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001463_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001463_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001465_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001465_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001467_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001467_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001468_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001468_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001469_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001469_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001470_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001470_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001475_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001475_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001478_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001478_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001480_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001480_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001483_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001483_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001486_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001486_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001490_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001490_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001501_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001501_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001503_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001503_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001504_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001504_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001505_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001505_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001509_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001509_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001511_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001511_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001512_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001512_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001515_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001515_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001516_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001516_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001518_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001518_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001519_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001519_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001520_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001520_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001521_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001521_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001592_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001592_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001594_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001594_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001595_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001595_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001596_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001596_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001597_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001597_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001598_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001598_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001599_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001599_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001600_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001600_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001601_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001601_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001602_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001602_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001604_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001604_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001605_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001605_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001607_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001607_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001609_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001609_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001611_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001611_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001615_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001615_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001616_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001616_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001617_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001617_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001623_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001623_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001628_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001628_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001629_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001629_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001630_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001630_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001632_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001632_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001633_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001633_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001643_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001643_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001644_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001644_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001646_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001646_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001647_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001647_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001664_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001664_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001665_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001665_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001705_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001705_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001706_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001706_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001708_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001708_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001709_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001709_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001711_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001711_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001713_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001713_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001715_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001715_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001716_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001716_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001717_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001717_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001718_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001718_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001721_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001721_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001724_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001724_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001725_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001725_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001728_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001728_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001730_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001730_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001747_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001747_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001749_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001749_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001750_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001750_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001751_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001751_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001752_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001752_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001753_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001753_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001754_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001754_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001755_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001755_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001757_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001757_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001759_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001759_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001761_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001761_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001762_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001762_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001764_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001764_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001765_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001765_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001766_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001766_tree_id.txt.tre
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001767_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0001767_tree_id.txt.tre
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