alterlab-phylogenetics

alterlab-phylogenetics is a Bioinformatics & life sciences skill for AI agents, published by AlterLab-IEU in the AlterLab-Academic-Skills repository on GitHub. Skillspace rates alterlab-phylogenetics F (45/100) and the safety scan rated it risky; the rating is based on static analysis only.

Build phylogenetic trees end-to-end from raw sequences — MAFFT multiple sequence alignment, optional TrimAl trimming, IQ-TREE 2 maximum-likelihood inference with model selection and bootstraps, FastTree for large datasets, then visualize with ETE3 or FigTree. Use when reconstructing trees from sequences (FASTA) for evolutionary analysis, microbial genomics, viral phylodynamics, protein-family studies, or molecular-clock dating. For manipulating/comparing an EXISTING Newick tree (prune, root, Robinson-Foulds, duplication/speciation events) use alterlab-etetoolkit; for plain sequence parsing/translation use alterlab-biopython. Part of the AlterLab Academic Skills suite.

Grade
F
Quality
45 / 100
Safety
Risky
GitHub stars
43

Unproven: rated by static analysis only, not yet compared head-to-head.

This rating describes the version of the repository we crawled; it may have changed since.

View source on GitHubAlterLab-IEU/AlterLab-Academic-Skills

Our review

Architecture
100 / 100
Maturity
Packaged: licensed, with a version or references
Security scan
High-risk patterns
License
MIT
Adoption
Adopted by 0 other repositories, in 0 collections

What the scanner flagged

  • executes shell/subprocess
  • over-broad allowed-tools ('*')

Not checked yet

  • Not judged on the rubric yet (not a contender in its category)
  • No blind task eval yet
  • Scope (portable / vendor / repo-internal) not assessed; only the top of each category is read for scope
  • Sibling files (scripts, references) not fetched; security scan covers SKILL.md only

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