scikit-bio

SUMMARY

What it does

This Agent Skill provides procedural knowledge for using the scikit-bio Python library in bioinformatics analyses. Based on the inspected SKILL.md source, it covers sequence manipulation (DNA/RNA/Protein, FASTA/FASTQ/GenBank I/O), pairwise and multiple sequence alignment (pair_align engine), phylogenetic tree construction and analysis (NJ, UPGMA, GME, BME, Newick I/O), alpha/beta diversity metrics (including Faith's PD and UniFrac), ordination methods (PCoA, CA, CCA, RDA), statistical tests (PERMANOVA, ANOSIM, Mantel, differential abundance), file I/O for 19+ biological formats, distance matrix handling, biological tables (BIOM, pandas/polars/AnnData dispatch), and protein embeddings. The skill declares compatibility with Python 3.10+, scikit-bio 0.7+, and NumPy 2.0+, and allows Read, Write, Edit, and Bash tools. The source record declares an MIT license, but the inspected SKILL.md frontmatter states BSD-3-Clause; this discrepancy is noted.