phylokit-mcp

Phylogenetic inference via IQ-TREE 3 — never returns a topology without its support

What does this entry provide?

phylokit-mcp is an MCP server entry in ChatHome Skills, sourced from Official MCP Registry and scored 78/100. As a Model Context Protocol server, it exposes tools that MCP-compatible LLM clients such as Claude, Cursor, and Copilot can call directly, extending an agent's reach beyond its built-in capabilities. ChatHome Skills discovered this entry through its daily ingest of official registries and GitHub discovery queries, and re-verifies repository facts, freshness signals, and install metadata on every run. The quality score weighs official-registry presence, a working install command, license clarity, GitHub star trajectory, and repository freshness — the full formula is on the Sources page. The install command above is ready to copy. Review the last-pushed date and repository status before adding phylokit-mcp to a production agent workflow; the snapshot facts below are point-in-time values from the most recent ingest.

Snapshot facts

Source: Official MCP Registry
Quality: 78/100
Install method: pypi
Repo: musharna/phylokit-mcp
Repo updated: Oct 26, 2026

Install command

uvx phylokit-mcp==0.8.0

Install method: pypi

Review the upstream source before running this command.

GitHub project

Quality

Repo stars

Repo updated

Oct 26, 2026

How is this score calculated?

Weighted across six dimensions, scored 0-100.
Provenance (25): listed in an official or curated registry.
Installability (25): a runnable install command beats a declared transport, which beats a source checkout.
Maintenance (20): recency of the last push; archived entries score zero here.
Adoption (20): repository stars on a log curve.
Documentation (10) and description quality (10): parsed manifest or SKILL.md frontmatter, and a real description rather than a placeholder.

MCP manifest

{
  "_meta": {
    "io.modelcontextprotocol.registry/official": {
      "status": "active",
      "isLatest": true,
      "updatedAt": "2026-10-26T21:41:03.893569Z",
      "publishedAt": "2026-10-26T21:41:03.893569Z",
      "statusChangedAt": "2026-10-26T21:41:03.893569Z"
    }
  },
  "server": {
    "name": "io.github.musharna/phylokit-mcp",
    "_meta": {
      "io.modelcontextprotocol.registry/publisher-provided": {
        "tool": "manual",
        "version": "0.8.0"
      }
    },
    "title": "phylokit-mcp",
    "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
    "version": "0.8.0",
    "packages": [
      {
        "version": "0.8.0",
        "transport": {
          "type": "stdio"
        },
        "identifier": "phylokit-mcp",
        "runtimeHint": "uvx",
        "registryType": "pypi",
        "registryBaseUrl": "https://pypi.org",
        "environmentVariables": [
          {
            "name": "OMP_NUM_THREADS",
            "description": "Pinned so inference is reproducible; overriding it makes IQ-TREE runs non-deterministic."
          },
          {
            "name": "MKL_NUM_THREADS",
            "description": "Pinned alongside OMP_NUM_THREADS for the same reproducibility reason."
          }
        ]
      }
    ],
    "repository": {
      "url": "https://github.com/musharna/phylokit-mcp",
      "source": "github"
    },
    "websiteUrl": "https://github.com/musharna/phylokit-mcp",
    "description": "Phylogenetic inference via IQ-TREE 3 — never returns a topology without its support"
  }
}

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