phylokit-mcp MCP Server

io.github.musharna/phylokit-mcp

Repository Registry

What is the phylokit-mcp MCP server?

Phylogenetic inference via IQ-TREE 3 — 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.

~/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>"
      }
    }
  }
}

Related MCP servers

Plant Genomics

Active

Plant genomics MCP — 56 tools across 23 backends with cross-source synthesis.

Python

MIT

View repository →

plantcv-mcp

Active

Plant phenotyping via PlantCV — returns traits plus the segmentation overlay they came from

Python

MIT

View repository →

tmodloader-mcp

Active

Drive a running tModLoader (Terraria) instance from an agent: launch, query, screenshot, read state.

Python

MIT

View repository →

breedsim-mcp

Active

Breeding-scheme simulation via AlphaSimR. Needs R, AlphaSimR and libtirpc-dev on the host.

Python

GPL-3.0

View repository →

Vox Pop

Active

Search 9 public discussion platforms for real opinions. Semantic routing, no API keys required.

Python

MIT

View repository →

TSUNAGI///Matrix — MAPPING

BMW E46 M3 MSS54HP DME: read bins and Testo logs, get VE and rf_korr corrections, all locally.

View repository →