PluginBench
MCP Server
Active
GPL-2.0

phylokit-mcp MCP Server

io.github.musharna/phylokit-mcp

RepositoryRegistry

What is the phylokit-mcp MCP server?

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

How to install phylokit-mcp

Copy-paste configuration for popular MCP clients.

transport: stdio
Config generated by PluginBench — verify against the source before use.
Environment / auth
  • 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.

Claude Desktop
~/Library/Application Support/Claude/claude_desktop_config.json
{
  "mcpServers": {
    "phylokit-mcp": {
      "command": "uvx",
      "args": [
        "phylokit-mcp"
      ],
      "env": {
        "OMP_NUM_THREADS": "<YOUR_OMP_NUM_THREADS>",
        "MKL_NUM_THREADS": "<YOUR_MKL_NUM_THREADS>"
      }
    }
  }
}
Cursor
~/.cursor/mcp.json
{
  "mcpServers": {
    "phylokit-mcp": {
      "command": "uvx",
      "args": [
        "phylokit-mcp"
      ],
      "env": {
        "OMP_NUM_THREADS": "<YOUR_OMP_NUM_THREADS>",
        "MKL_NUM_THREADS": "<YOUR_MKL_NUM_THREADS>"
      }
    }
  }
}
Windsurf
~/.codeium/windsurf/mcp_config.json
{
  "mcpServers": {
    "phylokit-mcp": {
      "command": "uvx",
      "args": [
        "phylokit-mcp"
      ],
      "env": {
        "OMP_NUM_THREADS": "<YOUR_OMP_NUM_THREADS>",
        "MKL_NUM_THREADS": "<YOUR_MKL_NUM_THREADS>"
      }
    }
  }
}
VS Code
.vscode/mcp.json
{
  "servers": {
    "phylokit-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "phylokit-mcp"
      ],
      "env": {
        "OMP_NUM_THREADS": "<YOUR_OMP_NUM_THREADS>",
        "MKL_NUM_THREADS": "<YOUR_MKL_NUM_THREADS>"
      }
    }
  }
}
Claude Code
claude mcp add phylokit-mcp --env OMP_NUM_THREADS=<YOUR_OMP_NUM_THREADS> --env MKL_NUM_THREADS=<YOUR_MKL_NUM_THREADS> -- uvx phylokit-mcp

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