{"slug":"mims-harvard-tooluniverse-phylogenetics","source_name":"mims-harvard/tooluniverse-phylogenetics","name":"Mims Harvard/Tooluniverse Phylogenetics","description":"Phylogenetic analysis — de novo multiple sequence alignment (Clustal Omega/MUSCLE/MAFFT via EBI_msa_align) and neighbour-joining/UPGMA tree building (EBI_build_phylogenetic_tree) from your own sequences, plus tree analysis, treeness, saturation (PhyKIT), parsimony-informative sites, alignment gap analysis, DVMC, long-branch detection, BUSCO orthologs. Uses PhyKIT, Biopython, DendroPy. Use to align a set of sequences, build a tree from sequences or an alignment, or for phylogenetic tree QC, multi","version":3,"lift":{"pass_rate_delta_pts":45.45,"pass_rate_pct":68.2,"total_cases":22,"passed_cases":15,"tokens_delta_pct":334.6,"turns_delta_pct":0,"verdict":"mixed","benchmark_model":"gemini-3.6-flash","grading_method":"judged","completed_at":"2026-08-09T17:11:30.788837+00:00"},"skill_score":0.6818,"benchmark_models":[{"model":"gemini-3.6-flash","headline":true,"delta_pts":45.45,"with_pass_pct":68.2,"without_pass_pct":22.7,"tokens_delta_pct":334.6,"turns_delta_pct":0,"total_cases":22,"cases_aggregated":16,"verdict":"mixed","never_hurt":false,"completed_at":"2026-08-09T17:11:30.788837+00:00","run_id":"969cf0b1-8b50-4ec4-bb6c-b84833f7aa98","version_number":3,"is_latest_version":true,"gate":null}],"trust":{"skill_safety":"passed","safety_status":"clean","intent_verdict":"safe","content_status":"clean","indexable":true},"license":"Apache-2.0","install_count":0,"manifest_hash":"cc5f00f196e63b83fb59a9c748b2cb0f138b27565a6a32191efb0c4ae5cdd1c6","raw_url":"https://app.decimal.ai/s/mims-harvard-tooluniverse-phylogenetics/SKILL.md","scorecard_url":"https://app.decimal.ai/skills/mims-harvard-tooluniverse-phylogenetics"}