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.

Install to Claude Code

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