alterlab-phylogenetics

87 / 100 · Low risk

Fine to try.

By AlterLab-IEU/AlterLab-Academic-Skills (GitHub) · research · 87 stars · scanned at commit 3ab6d03

Build phylogenetic trees end-to-end from raw sequences — MAFFT multiple sequence alignment, optional TrimAl trimming, IQ-TREE 3 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, Ro…

Works with any agent that supports SKILL.md skills.

Partially scanned — some files couldn't be read; we'll retry on the next scan

What this skill can do

Runs commands on your computer

The author does not mention this.

Found in 5 places.

skills/bioinformatics/alterlab-phylogenetics/SKILL.md, line 27conda install -c bioconda mafft iqtree fasttree trimal # iqtree is now IQ-TREE 3
skills/bioinformatics/alterlab-phylogenetics/SKILL.md, line 105result = subprocess.run(cmd, stdout=out, stderr=subprocess.PIPE, text=True)
skills/bioinformatics/alterlab-phylogenetics/SKILL.md, line 138result = subprocess.run(cmd, capture_output=True, text=True)

Show 2 more

skills/bioinformatics/alterlab-phylogenetics/SKILL.md, line 181result = subprocess.run(cmd, capture_output=True, text=True)
skills/bioinformatics/alterlab-phylogenetics/SKILL.md, line 237result = subprocess.run(cmd, stdout=out, stderr=subprocess.PIPE, text=True)

Downloads and installs other software

This is disclosed by the author in the skill's SKILL.md or README.

Found in 3 places.

skills/bioinformatics/alterlab-phylogenetics/SKILL.md, line 29brew install mafft fasttree
skills/bioinformatics/alterlab-phylogenetics/SKILL.md, line 30brew tap brewsci/bio && brew install brewsci/bio/iqtree brewsci/bio/trimal
skills/bioinformatics/alterlab-phylogenetics/SKILL.md, line 33uv pip install "ete3==3.1.3" # also needs numpy<2 and PyQt5 for rendering

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'alterlab-phylogenetics' ] || [ -L ~/.agents/skills/'alterlab-phylogenetics' ]; then echo 'A skill folder named alterlab-phylogenetics already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/AlterLab-IEU/AlterLab-Academic-Skills' "$d" && git -C "$d" checkout --quiet '3ab6d034385ec4fedc3f6f4099292d4e91f60300' -- 'skills/bioinformatics/alterlab-phylogenetics' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bioinformatics/alterlab-phylogenetics' ~/.agents/skills/'alterlab-phylogenetics' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'alterlab-phylogenetics' ~/.claude/skills/'alterlab-phylogenetics' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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Score history

Date	Version	Score
2026-11-07	`3ab6d03`	87