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.
Install
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-phylogeneticsnpx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-phylogenetics -a claude-code -gnpx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-phylogenetics -a codex -ggemini skills install https://github.com/AlterLab-IEU/AlterLab-Academic-Skills.git --path skills/bioinformatics/alterlab-phylogeneticsgh skill install AlterLab-IEU/AlterLab-Academic-Skills alterlab-phylogeneticsgit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-Skills /tmp/AlterLab-IEU__AlterLab-Academic-Skills
mkdir -p ~/.claude/skills ~/.agents/skills
cp -R /tmp/AlterLab-IEU__AlterLab-Academic-Skills/skills/bioinformatics/alterlab-phylogenetics ~/.claude/skills/alterlab-phylogenetics # Claude Code
cp -R /tmp/AlterLab-IEU__AlterLab-Academic-Skills/skills/bioinformatics/alterlab-phylogenetics ~/.agents/skills/alterlab-phylogenetics # Codex, Cursor, Gemini CLI, Copilot, OpenCode