Phylogenetics

This covers the standard phylogenetics pipeline: MAFFT for multiple sequence alignment, IQ-TREE 2 for maximum likelihood tree inference with automatic model selection, and FastTree when you've got thousands of sequences and need speed over precision. The code is straightforward Python wrappers around command line tools, with ETE3 for tree manipulation and viz. Use it for viral outbreak tracing, microbial genomics, protein family analysis, or molecular clock studies. The workflow is solid and the model selection guidance is helpful (TEST mode for auto, then GTR+G for DNA or LG+G4 for proteins). One thing: you'll need conda and bioconda set up properly, and the trimming step with TrimAl is optional but worth doing to remove poorly aligned regions before tree building.

skills.sh installs: 2K
GitHub stars: 56.6K
last updated: Aug 21, 2026

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Install

$ npx -y skills add k-dense-ai/scientific-agent-skills --skill phylogenetics --agent claude-code

Installs into .claude/skills of the current project.

Files

Phylogenetics

When to use

Use this workflow for an alignment of homologous loci or proteins, a gene tree, branch support, and an interpretable tree figure. Multi-locus partitioning, concordance factors, ancestral states and dating are covered in IQ-TREE reference.

A gene tree does not establish a species tree, transmission direction, or horizontal transfer by itself. Sampling dates alone do not justify a molecular clock.

Versions and installation

Reviewed against current official documentation on 2026-10-01. The executed smoke workflow used MAFFT 7.526, IQ-TREE 3.1.4, FastTree 2.2.0 and ETE3 3.1.3 on Python 3.12. ETE3 remains deliberate for this helper; ETE4 is a separate API and is not a drop-in replacement. ETE3 imports cgi, removed in Python 3.13. The native executables are not Python packages.

Illustrative installation commands; verify executable versions after installation:

SKILL.md on GitHub