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scikit-bio

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A Python bioinformatics toolkit for sequence, phylogeny, and microbiome/community-ecology analysis; use it when you need to compute diversity/ordination/statistics from biological data and standard formats (FASTA/FASTQ/Newick/BIOM).

scientific-skills/Data Analysis/scikit-bio/SKILL.md

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Sep 17, 2026
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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

## When to Use

- You need to parse, validate, and manipulate biological sequences (DNA/RNA/protein) and their metadata.
- You are running microbiome/community-ecology workflows (alpha/beta diversity, UniFrac, ordination, PERMANOVA).
- You need to build, transform, or compare phylogenetic trees (Newick I/O, pruning/rerooting, patristic distances).
- You want to compute and work with distance matrices and downstream multivariate analyses (PCoA, Mantel, ANOSIM).
- You need to read/write common bioinformatics formats (FASTA/FASTQ, Newick, BIOM) and convert between them.

## Key Features

- **Sequence objects**: `DNA`, `RNA`, `Protein`, and generic `Sequence` with validation, slicing, motif search, reverse complement, transcription/translation, and metadata handling.
- **Alignment utilities**: pairwise local alignment (SSW-based) and multiple sequence alignment containers (`TabularMSA`) with consensus support.
- **Phylogenetics**: `TreeNode` manipulation, tree construction from distance matrices (e.g., Neighbor Joining), and tree distance/metrics.
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