phylokit-mcp MCP Server

by musharna Your server? Claim it

local only

phylokit-mcp runs on your own machine — the client starts it, so there is no endpoint to ping. 112 installs a week from pypi. Last commit 17 Sep 2026.

Phylogenetic inference via IQ-TREE 2 — never returns a topology without its support

Installs per day peak 64 · avg 23 · -24% w/w

a month agotoday

112

Installs / week

pypi · phylokit-mcp

Stars

0 open issues

17 Sep 2026

Last commit

0 releases in 90 days

GPL-2.0

License

Python

Nothing serious here today

Today is the operative word: we check phylokit-mcp every 15 minutes and re-read its code on every release. Watch it and you find out the day that stops being true.

Connect this server

This server runs on your own machine — install it with the package manager and the client starts it for you. Package name taken from the official registry entry.

Claude Code Claude Desktop Codex Cursor VS Code

run in your terminal

claude mcp add phylokit-mcp -- uvx phylokit-mcp

~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "phylokit-mcp": {
      "args": [
        "phylokit-mcp"
      ],
      "command": "uvx"
    }
  }
}

~/.codex/config.toml

[mcp_servers.phylokit-mcp]
command = "uvx"
args = ["phylokit-mcp"]

.cursor/mcp.json

{
  "mcpServers": {
    "phylokit-mcp": {
      "args": [
        "phylokit-mcp"
      ],
      "command": "uvx"
    }
  }
}

.vscode/mcp.json

{
  "mcpServers": {
    "phylokit-mcp": {
      "args": [
        "phylokit-mcp"
      ],
      "command": "uvx"
    }
  }
}

This one needs environment variables set before it will start: OMP_NUM_THREADS (Pinned so inference is reproducible; overriding it makes IQ-TREE runs non-deterministic.), MKL_NUM_THREADS (Pinned alongside OMP_NUM_THREADS for the same reproducibility reason.). The author declared them in the registry entry; get the values from the project itself.

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phylokit-mcp — questions

Answers built from our own checks of this server.

Why is there no uptime for phylokit-mcp?

phylokit-mcp runs on your own machine over stdio — there is no network address to reach, so uptime cannot be measured for it by anyone. What can be measured is adoption: the pypi package phylokit-mcp was installed 112 times last week.

How do I connect phylokit-mcp?

Copy the ready config from this page — we generate it for Claude Code, Claude Desktop, Codex, Cursor and VS Code, each with the file path that client actually reads. It runs locally, so the command pulls phylokit-mcp straight from pypi; nothing to host, nothing to sign up for.

How many people use phylokit-mcp?

The pypi package phylokit-mcp was installed 112 times in the last week. Week over week that is -24%. We show installs rather than GitHub stars on purpose: a star is a bookmark, an install is someone actually running it.

Is phylokit-mcp open source?

Yes — it is published under the GPL-2.0 licence, written in Python and 0 stars on GitHub. The source link is on this page, so you can read exactly what it does with your data before you connect it.