---
title: "Phylogenetics - Air Market"
description: "You have a set of biological sequences and you want to know how they are related to each other. This walks through lining them up, building a family tree from them, and turning that tree into a pictu…"
canonical: "https://airmarket.ai/app/phylogenetics"
---

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

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

# Phylogenetics

Turn a pile of sequences into a tree you can read

## What this does

You have a set of biological sequences and you want to know how they are related to each other. This walks through lining them up, building a family tree from them, and turning that tree into a picture. Useful for evolution questions, microbial genomes, tracking virus spread, protein families and dating divergence.

### Top 3 things it does for you

- Align a set of sequences
- Build a tree by maximum likelihood or a faster method
- Draw the tree so it can be looked at

## Information

**Phylogenetics 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 | 1.2 |
| Size | 28 KB |
| Licence | MIT |
| Repository | [k-dense-ai/scientific-agent-skills](https://github.com/k-dense-ai/scientific-agent-skills/tree/ad21a3868923628330734375dddbf7b86ea84222/skills/phylogenetics) |
| GitHub stars | 34,239 (as of Nov 2026) |

## Security report

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

**What Phylogenetics's check was run against**

|  |  |
| --- | --- |
| Commit | ad21a3868923628330734375dddbf7b86ea84222 |
| Content hash | a104551df2ffed037a6554c901a065e741ea38e2e860f50a2d1e460aa8dad2bd |
| Files read | [Browse the files at this exact commit](https://github.com/k-dense-ai/scientific-agent-skills/blob/ad21a3868923628330734375dddbf7b86ea84222/skills/phylogenetics/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 Phylogenetics](/security/phylogenetics)

## About Phylogenetics

Building a phylogenetic tree means stringing several tools together. This skill covers that path: MAFFT for multiple alignment, then IQ-TREE 2 when you want maximum likelihood or FastTree when you want a fast neighbour-joining or ML tree.

Once the tree exists it needs looking at, and the skill covers visualising it with ETE3 or FigTree.

It is aimed at evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis and molecular clock studies.

## What's inside

- SKILL.md - instructions
- references/iqtree_inference.md - reference
- scripts/phylogenetic_analysis.py - script

## Questions

### Is Phylogenetics safe to install?

AIR scanned this exact version of Phylogenetics and flagged nothing. AIR's verdict: safe. The verdict is named by the content that was read, at commit ad21a3868923, so it cannot drift onto a version nobody scanned. The full report is at https://airmarket.ai/security/phylogenetics.

### How do I install Phylogenetics?

Open https://airmarket.ai/app/phylogenetics 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/ad21a3868923628330734375dddbf7b86ea84222/skills/phylogenetics. 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/phylogenetics>