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mcp/harbor
Gemini CLI

phylokit-mcp for Gemini CLI

io.github.musharna/phylokit-mcp

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

client:Gemini CLI transport:stdio runtime:pypi

Install phylokit-mcp in Gemini CLI

~/.gemini/settings.json · windows: %USERPROFILE%\.gemini\settings.json

Held in this page only — never stored, logged, or sent anywhere but back to your screen. 

{
  "mcpServers": {
    "phylokit-mcp": {
      "command": "uvx",
      "args": [
        "phylokit-mcp"
      ],
      "env": {
        "OMP_NUM_THREADS": "<OMP_NUM_THREADS>",
        "MKL_NUM_THREADS": "<MKL_NUM_THREADS>"
      }
    }
  }
}

Gemini expands $VAR and ${VAR} inside env values, so a secret can live in your shell rather than this file. Gemini CLI docs

phylokit-mcp in other clients

phylokit-mcp MCP server