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phylokit-mcp for VS Code

io.github.musharna/phylokit-mcp

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

client:VS Code transport:stdio runtime:pypi

Install phylokit-mcp in VS Code

.vscode/mcp.json 

{
  "inputs": [
    {
      "type": "promptString",
      "id": "omp-num-threads",
      "description": "OMP_NUM_THREADS",
      "password": true
    },
    {
      "type": "promptString",
      "id": "mkl-num-threads",
      "description": "MKL_NUM_THREADS",
      "password": true
    }
  ],
  "servers": {
    "phylokit-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "phylokit-mcp"
      ],
      "env": {
        "OMP_NUM_THREADS": "${input:omp-num-threads}",
        "MKL_NUM_THREADS": "${input:mkl-num-threads}"
      }
    }
  }
}

VS Code prompts for each input the first time the server starts, so no secret is written to the file. VS Code docs

phylokit-mcp in other clients

phylokit-mcp MCP server