---
title: "Scikit Bio - Air Market"
description: "You have sequence data from a microbiome study and need the usual analyses done. This toolkit covers alignments and trees, the diversity measures people expect to see, ordination and group testing, p…"
canonical: "https://airmarket.ai/app/scikit-bio"
---

[Air Market](/) / [Data & Analytics](/category/data) / Scikit Bio

Skill by [K-Dense](/@k-dense-ai)

# Scikit Bio

Standard microbiome analysis, from sequences to diversity

## What this does

You have sequence data from a microbiome study and need the usual analyses done. This toolkit covers alignments and trees, the diversity measures people expect to see, ordination and group testing, plus reading and writing the standard file formats.

### Top 3 things it does for you

- Align sequences and build phylogenetic trees
- Compute alpha, beta and UniFrac diversity
- Run PCoA ordination and PERMANOVA

## Information

**Scikit Bio at a glance**

|  |  |
| --- | --- |
| Kind | Skill |
| Publisher | [K-Dense](/@k-dense-ai) |
| Category | [Data & Analytics](/category/data) |
| Works with | Agent Skills - an open standard supported by 40+ agents |
| Version | 1.1 |
| Size | 39 KB |
| Licence | MIT |
| Repository | [k-dense-ai/scientific-agent-skills](https://github.com/k-dense-ai/scientific-agent-skills/tree/93124850ef08487e423165554c54f0b333d5631d/skills/scikit-bio) |
| GitHub stars | 34,239 (as of Nov 2026) |

## Security report

**Verified.** AIR scanned this exact version of Scikit Bio and flagged nothing. AIR's verdict: **safe**.

**What Scikit Bio's check was run against**

|  |  |
| --- | --- |
| Commit | 93124850ef08487e423165554c54f0b333d5631d |
| Content hash | e3f2db1810b3bd0c119e2b05863badc6b6013a76688e18e686f5f769d4b4a331 |
| Files read | [Browse the files at this exact commit](https://github.com/k-dense-ai/scientific-agent-skills/blob/93124850ef08487e423165554c54f0b333d5631d/skills/scikit-bio/SKILL.md) |

A scan is named by the exact content it read, not by a version number. A different version is a different artifact, and nothing here applies to a version AIR has not scanned.

[Read the full security report for Scikit Bio](/security/scikit-bio)

## About Scikit Bio

A toolkit for biological data, oriented toward microbiome analysis. It handles sequence analysis, alignments and phylogenetic trees.

On the community side it covers alpha and beta diversity metrics including UniFrac, ordination via PCoA, and PERMANOVA, with FASTA and Newick input and output.

## What's inside

- SKILL.md - instructions
- references/api_reference.md - reference

## Questions

### Is Scikit Bio safe to install?

AIR scanned this exact version of Scikit Bio and flagged nothing. AIR's verdict: safe. The verdict is named by the content that was read, at commit 93124850ef08, so it cannot drift onto a version nobody scanned. The full report is at https://airmarket.ai/security/scikit-bio.

### How do I install Scikit Bio?

Open https://airmarket.ai/app/scikit-bio on Air Market and use the install action: Air Market hands Claude a prompt naming this exact skill, and Claude sets it up. Source, pinned to the exact commit this listing describes: https://github.com/k-dense-ai/scientific-agent-skills/tree/93124850ef08487e423165554c54f0b333d5631d/skills/scikit-bio. Install from that link, not the branch.

## Related on Air Market

- [More Data & Analytics listings](/category/data)
- [Everything by K-Dense](/@k-dense-ai)

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Canonical URL: <https://airmarket.ai/app/scikit-bio>