Koskamo

phylokit-mcp

An MCP server enabling AI agents to perform phylogenetic inference using IQ-TREE 3 and sequence alignment with MAFFT. It ensures every returned topology includes bootstrap support values, reports conflicting clades, ranks substitution models by AIC/BIC, and compares trees using Robinson-Foulds distance. It supports tools for inferring trees, selecting models, comparing topologies, simulating alignments, and mapping residues.

Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

phylokit-mcp logo, by musharnaCommunity listingLocal stdioSource reviewed; not executedPublished by musharna
Vendor documentation

What you can do with it

  • Build maximum-likelihood phylogenetic trees with bootstrap support
  • Align unaligned FASTA sequences using MAFFT
  • Rank substitution models using AIC/AICc/BIC criteria
  • Compare phylogenetic trees using Robinson-Foulds distance

Source and maintenance

Community listingRegistry 0.8.0
mcp-registry: io.github.musharna/phylokit-mcp@0.8.0Source repositoryProject website
Maintenance checked

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

phylokit-mcp 0.8.0

pypiuvx
phylokit-mcp package definition
{
  "version": "0.8.0",
  "transport": "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."
    }
  ]
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

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Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.
Cursor configuration
{
  "mcpServers": {
    "phylokit-mcp": {
      "command": "uvx",
      "args": [
        "phylokit-mcp==0.8.0"
      ],
      "env": {
        "OMP_NUM_THREADS": "<YOUR_OMP_NUM_THREADS>",
        "MKL_NUM_THREADS": "<YOUR_MKL_NUM_THREADS>"
      }
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.
Cline configuration
{
  "mcpServers": {
    "phylokit-mcp": {
      "command": "uvx",
      "args": [
        "phylokit-mcp==0.8.0"
      ],
      "env": {
        "OMP_NUM_THREADS": "<YOUR_OMP_NUM_THREADS>",
        "MKL_NUM_THREADS": "<YOUR_MKL_NUM_THREADS>"
      }
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.
VS Code configuration
{
  "servers": {
    "phylokit-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "phylokit-mcp==0.8.0"
      ],
      "env": {
        "OMP_NUM_THREADS": "<YOUR_OMP_NUM_THREADS>",
        "MKL_NUM_THREADS": "<YOUR_MKL_NUM_THREADS>"
      }
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.
Claude Desktop configuration
{
  "mcpServers": {
    "phylokit-mcp": {
      "command": "uvx",
      "args": [
        "phylokit-mcp==0.8.0"
      ],
      "env": {
        "OMP_NUM_THREADS": "<YOUR_OMP_NUM_THREADS>",
        "MKL_NUM_THREADS": "<YOUR_MKL_NUM_THREADS>"
      }
    }
  }
}

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