scikit-bio

SKILL.md

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