scikit-bio
Installation
SKILL.md
scikit-bio
A Python library for biological data analysis spanning sequence handling, phylogenetics, microbial ecology, and multivariate statistics.
When to Apply
Use this skill when users need to:
| Task Category | Examples |
|---|---|
| Sequence work | DNA/RNA/protein manipulation, motif finding, translation |
| File handling | FASTA, FASTQ, GenBank, Newick, BIOM I/O |
| Alignments | Pairwise or multiple sequence alignment |
| Phylogenetics | Tree construction, manipulation, distance calculations |
| Diversity metrics | Alpha diversity (Shannon, Faith's PD), beta diversity (Bray-Curtis, UniFrac) |
| Ordination | PCoA, CCA, RDA for dimensionality reduction |
| Statistical tests | PERMANOVA, ANOSIM, Mantel tests |
| Microbiome analysis | Feature tables, rarefaction, community comparisons |