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scikit-bio

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Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

skills/scikit-bio/SKILL.md

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# scikit-bio

## Overview

Targets scikit-bio 0.7.4. Use it for sequence manipulation, alignment, phylogenetics, microbial ecology, and multivariate statistics. Native tests exercise small synthetic fixtures; examples with filenames or undefined inputs are workflow templates. See [review evidence and boundaries](references/review.md).

## When to Use This Skill

This skill should be used when the user:
- Works with biological sequences (DNA, RNA, protein)
- Needs to read/write biological file formats (FASTA, FASTQ, GenBank, Newick, BIOM, etc.)
- Performs sequence alignments or searches for motifs
- Constructs or analyzes phylogenetic trees
- Calculates diversity metrics (alpha/beta diversity, UniFrac distances)
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