phylogenetics

SUMMARY

What it does

This skill provides a pipeline for phylogenetic analysis, including multiple sequence alignment with MAFFT, maximum likelihood tree inference with IQ-TREE 2, fast approximate ML with FastTree, and tree visualization and analysis with ETE3. It includes Python functions for each step, a complete analysis script, and guidance on model selection and best practices. The skill is designed for evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.