Phylogenetics

A comprehensive reference skill for scikit-bio, a Python bioinformatics library. Provides documentation and code examples for biological sequence manipulation, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination analysis (PCoA, CCA), statistical tests (PERMANOVA, ANOSIM), and microbiome data processing with FASTA/BIOM file format support.

A comprehensive phylogenetic tree analysis toolkit built on ETE (Environment for Tree Exploration). It enables tree manipulation (loading, pruning, rooting), evolutionary analysis (detecting duplications and speciations, ortholog/paralog identification), NCBI taxonomy integration, and publication-quality visualization in PDF/SVG/PNG formats. Ideal for phylogenomics research and clustering analysis.