# phylokit-mcp

> phylokit-mcp — musharna-phylokit-mcp. Use this tool when you need to perform phylogenetic inference and analysis, solving problems such as determining evolutionary relationships and assessing model uncertainty. It takes in alignment data and returns detailed diagnostics, including per-clade bootstrap support, model selection, and tree comparison. Ideal for use in molecular biology and evolutionary biology research contexts.

Canonical page: https://skillsregistry.net/skills/musharna-phylokit-mcp  
JSON: https://api.skillsregistry.net/v1/skills/musharna-phylokit-mcp

## Description

Phylogenetic inference server driving IQ-TREE 2, always returning per-clade bootstrap support plus model selection, tree comparison, and alignment simulation, with detailed diagnostics like conflicting clades and model uncertainty.

## Trust

- **Trust score (0–1):** 0.70
- **Verification tier:** verified
- **Last scanned:** 2026-08-29

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** other
- **Updated:** 2026-08-29

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/l7jt2o8tqk)
- **Repository:** <https://github.com/musharna/phylokit-mcp>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "musharna-phylokit-mcp"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/musharna-phylokit-mcp` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/musharna-phylokit-mcp/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt