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Opentreeoflife

Resolve scientific names, inspect Open Tree of Life taxa, and find common ancestors by taxon ID.

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Install Opentreeoflife

Pick your client, then add it in one click or paste the config.

STDIONode.js
~/Library/Application Support/Claude/claude_desktop_config.json
claude_desktop_config.json
{
  "mcpServers": {
    "opentreeoflife": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-opentreeoflife"
      ]
    }
  }
}

Settings → Developer → Edit Config, merge this into mcpServers, then fully quit and reopen Claude Desktop.

Automated check passed— started and listed 3 tools correctly (1d ago).

Overview

The Opentreeoflife MCP server resolves scientific names against the Open Tree of Life and returns taxon IDs, accepted names, ranks, and match flags. Use those IDs to retrieve taxon metadata and full ancestry lineages, or to find the most recent common ancestor of 2–10 taxa. It provides three keyless tools and can run through the Pipeworx gateway or as a local stdio process. Reach for it when an agent needs taxonomic lookup or lineage comparisons from Open Tree of Life data.

Use cases

  • Resolve Latin binomial names to Open Tree of Life taxon IDs
  • Inspect taxon synonyms and ancestry lineages
  • Compare taxa through their most recent common ancestor
  • Normalize scientific names before downstream taxonomic queries

Key features

  • Scientific-name matching with synonym and approximation flags
  • Taxon metadata and complete ancestry retrieval
  • Most recent common ancestor queries for 2–10 taxa
  • Keyless MCP tools
  • Hosted gateway and local stdio modes

Tools3

What Opentreeoflife lets your agent do. Expand a tool for its parameters.

Verified live~319 tokens of context

Security & health

What it can reach and how reliably it runs — from our own checks, not the maintainer’s claims.

ActiveLast checked 3d ago

Recent health check succeeded.

4/4 checks healthy over the last 47d

What it can do

From the 3 tools this server returned when we ran it.

Read-only tools · 3
Network at startup3 connections
Files written at startupNone
Install scriptsNone
npm provenanceSigned build
Package age134 days
Maintainers1

Observed 2026-10-23 in an isolated sandbox. A description of reach, not a security audit.

Supply-chain signal

No high-severity advisories surfaced by our automated scan.

Critical 0High 0Medium 0Low 0

Scanned 15d ago via OSV.dev · @pipeworx/mcp-opentreeoflife (npm)

Adoption & maintenance

Factual signals from GitHub, npm, and our automated checks — not a rating.

npm downloads436Package downloads in the last 30 days.
Last commit28d agoMost recent push to the default branch.
Availability100%Our rolling endpoint + install checks that succeeded.
Install checkPassedOur sandbox started it and listed its tools.
Tools exposed3Callable tools this server registers over MCP.
Directory activity1 viewsConfig copies, upvotes, and views on AllMCPs.

How Opentreeoflife works

What Opentreeoflife MCP server does

The Opentreeoflife MCP server gives agents access to taxonomic data from the Open Tree of Life. Its workflow begins with scientific-name resolution: match_names accepts Latin binomial names and returns the best match for each, including the Open Tree of Life taxon identifier (ott_id), accepted name, rank, and indicators for synonyms or approximate matches.

The returned ott_id is the input for the other taxon-specific operations. taxon_info uses it to return an accepted name, rank, unique name, synonyms, source taxonomy, and the complete ancestry from the selected taxon to the root of life. common_ancestor accepts 2–10 taxon IDs and identifies their most recent common ancestor in the synthetic Tree of Life.

How it works

The Opentreeoflife MCP server exposes the three tools over MCP. A typical agent workflow is:

  1. Send one or more scientific names to match_names.
  2. Review the returned IDs and match-quality flags.
  3. Pass a selected ID to taxon_info, or pass multiple IDs to common_ancestor.

All three listed tools are keyless. The server can be reached through the Pipeworx scoped endpoint at https://gateway.pipeworx.io/opentreeoflife/mcp, which also exposes shared Pipeworx meta-tools. Those additional gateway tools can route broader questions across the Pipeworx catalog. Alternatively, the full gateway endpoint lists the wider catalog directly.

Setup and configuration

For a hosted MCP connection, add the scoped URL to a client configuration under the opentreeoflife server name. The README specifically shows Claude Desktop, Cursor, and Windsurf as supported setup examples.

A local installation is also available through the @pipeworx/mcp-opentreeoflife package. Configure an MCP client to run it with npx -y @pipeworx/mcp-opentreeoflife, or execute that command directly to verify startup. The local process communicates through standard input and output and exposes only this pack's three tools, without the gateway's shared meta-tools. No environment variables are documented as required.

The same hosted tools can be called without an MCP client through the Pipeworx HTTP API. For example, send a JSON POST request to /v1/tools/match_names with a names array.

Tools and capabilities

  • match_names: resolve scientific names to Open Tree of Life IDs and report match details.
  • taxon_info: inspect taxon metadata, synonyms, source taxonomy, and full lineage.
  • common_ancestor: find the most recent common ancestor for 2–10 taxa.

The Opentreeoflife MCP server is suited to taxonomic normalization, lineage inspection, and comparisons among known taxa. It does not require API keys for the listed tools, and the documented operations depend on IDs returned by name matching for subsequent lookups.

Limitations and notes

Name matching should generally come first because taxon_info and common_ancestor require ott_id values. common_ancestor is limited to between two and ten taxa per request. Gateway connections list shared Pipeworx tools in addition to the pack's own tools, so the visible tool count can exceed the three operations documented here. A local stdio connection avoids those shared gateway tools but also does not provide gateway-wide routing.

Read the full README View source on GitHub

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Frequently Asked Questions about Opentreeoflife

Opentreeoflife is an MCP server that connects AI agents to Open Tree of Life data through match_names, taxon_info, and common_ancestor. It resolves scientific names to ott_ids, returns taxon details and ancestry, and finds the most recent common ancestor for 2–10 taxa. The listed tools require no API key.

Install it locally by configuring your MCP client to run `npx -y @pipeworx/mcp-opentreeoflife`. The package communicates over stdin and stdout. You can also connect to the hosted endpoint at `https://gateway.pipeworx.io/opentreeoflife/mcp` instead of running the package locally.

Call `match_names` with one or more scientific names. It returns the best match for each name, including the `ott_id`, accepted name, rank, and synonym or approximate-match flags. Use the returned `ott_id` with `taxon_info` or `common_ancestor`.

Yes. Call `common_ancestor` with the `ott_id` values for 2–10 taxa. The tool returns the most recent common ancestor in the synthetic Tree of Life, including its taxon ID, name, and rank.

Yes. The README includes Cursor among the MCP clients that can connect to the hosted Opentreeoflife endpoint. Add `https://gateway.pipeworx.io/opentreeoflife/mcp` to the client's MCP server configuration.

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