> ## Documentation Index
> Fetch the complete documentation index at: https://docs.kalarislabs.com/llms.txt
> Use this file to discover all available pages before exploring further.

# scikit-bio — AI agent skill for life sciences

> Python library scikit-bio for biological sequence and community-ecology analysis: DNA/RNA/protein sequences, pair_align alignment, phylogenetic trees (NJ,…

# `scikit-bio`

> Python library scikit-bio for biological sequence and community-ecology analysis: DNA/RNA/protein sequences, pair\_align alignment, phylogenetic trees (NJ, UPGMA, GME/BME, Newick), alpha/beta diversity including Faith's PD and UniFrac, PCoA/CCA/RDA ordination, PERMANOVA/ANOSIM/Mantel tests, ancom and dirmult differential abundance, BIOM tables, and FASTA/FASTQ/GenBank I/O. Use when computing microbiome diversity from a BIOM or feature table. Use when running PCoA and PERMANOVA on a distance matrix. Use when building or comparing phylogenetic trees from sequences. Use when reading, converting, or aligning FASTA/FASTQ/GenBank/Newick data. Use when testing differential abundance in compositional count data. Not for general-purpose sequence scripting where Biopython is enough.

**Category:** [life-sciences](/research-agent-skills/skills#life-sciences) · **License:** BSD-3-Clause license · **Version:** 1.2

## Install

```bash theme={null}
npx research-agent-skills install scikit-bio
npx skills add KalarisLabs/research-agent-skills --skill scikit-bio
```

## When to use it

Python library scikit-bio for biological sequence and community-ecology analysis: DNA/RNA/protein sequences, pair\_align alignment, phylogenetic trees (NJ, UPGMA, GME/BME, Newick), alpha/beta diversity including Faith's PD and UniFrac, PCoA/CCA/RDA ordination, PERMANOVA/ANOSIM/Mantel tests, ancom and dirmult differential abundance, BIOM tables, and FASTA/FASTQ/GenBank I/O. Use when computing microbiome diversity from a BIOM or feature table. Use when running PCoA and PERMANOVA on a distance matrix. Use when building or comparing phylogenetic trees from sequences. Use when reading, converting, or aligning FASTA/FASTQ/GenBank/Newick data. Use when testing differential abundance in compositional count data. Not for general-purpose sequence scripting where Biopython is enough.

## Full playbook

Read [SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/main/skills/scikit-bio/SKILL.md) for the complete workflow, references and any scripts. The agent installer copies the full skill folder.