Scikit Bio

If you're doing microbiome analysis or computational biology in Python, this wraps up the grunt work of sequence manipulation, phylogenetic trees, and diversity calculations. It handles the format hell of FASTA, FASTQ, Newick, and BIOM files, plus gives you UniFrac distances, PCoA ordination, and PERMANOVA tests without reaching for five different packages. The API is clean for common tasks like reverse complements, sequence alignment, and alpha/beta diversity metrics. It's not as comprehensive as Biopython for every conceivable biological format, but for microbial ecology and community analysis workflows, it's more focused and gets you to publication figures faster.

skills.sh installs: 297
GitHub stars: 33.2K
last updated: Aug 21, 2026

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Install

$ npx -y skills add davila7/claude-code-templates --skill scikit-bio --agent claude-code

Installs into .claude/skills of the current project.

Files

scikit-bio

Overview

scikit-bio is a comprehensive Python library for working with biological data. Apply this skill for bioinformatics analyses spanning sequence manipulation, alignment, phylogenetics, microbial ecology, and multivariate statistics.

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)
Performs ordination analysis (PCoA, CCA, RDA)
Runs statistical tests on biological/ecological data (PERMANOVA, ANOSIM, Mantel)
Analyzes microbiome or community ecology data
Works with protein embeddings from language models
Needs to manipulate biological data tables