FigTreeKit-MCP

analyze_taxonomy

Test monophyly for every group at a given taxonomic rank in a phylogenetic tree using taxon labels or a mapping file.

Instructions

Analyze monophyly of all groups at a given taxonomic rank.

Equivalent to figtreekit --analyze-taxonomy RANK. Requires terminal labels carrying taxonomy info, or a whitelisted mapping file.

Args: tree_content: Newick/Nexus content. tree_file: Path to a tree file inside an allowed read root. rank: Taxonomic rank to analyze (domain..species). taxonomy_mapping_file: Optional CSV/TSV mapping (whitelisted). taxonomy_levels: prefix:rank list. group_size_min: Only report groups with at least this many taxa.

Tool call template

This tool declares no required parameters. Add optional parameters from the input schema as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {},
    "name": "analyze_taxonomy"
  }
}

Input Schema

Name	Required	Description	Default
`rank`	No
`tree_file`	No
`tree_content`	No
`group_size_min`	No
`taxonomy_levels`	No
`taxonomy_mapping_file`	No

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Oct 20, 2026

TDQS

A3.6/5.0

Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description carries the full burden. It discloses useful behavioral context: the taxonomy-label/mapping-file prerequisite and the whitelist/allowed-read-root security constraint on files. It is silent, however, on whether the operation is read-only and on any rate/side-effect behavior (return shape is covered by the output schema).

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Front-loaded with the core purpose, followed by the CLI equivalent and an efficient Args block. The figtreekit equivalence line is somewhat expendable, but overall it is tight and well structured with little waste.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given six params, 0% schema coverage, and an existing output schema, the description covers prerequisites, security constraints, and every parameter, so it is largely self-sufficient. It stops short of an explicit sibling note, which is the only real gap for an agent choosing between this and check_monophyly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, yet the description compensates well by documenting all six parameters, including format hints (Newick/Nexus content, domain..species for rank, CSV/TSV for the mapping file, prefix:rank list, minimum group size). This meaningfully exceeds the raw schema, though a couple of entries remain terse.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb+resource+scope: "Analyze monophyly of all groups at a given taxonomic rank." This is clearly distinguishable in scope from a general clade checker, but it never explicitly names or contrasts with the close sibling check_monophyly or taxonomy_completeness. Clear purpose, missing explicit sibling differentiation.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Provides a meaningful precondition ("Requires terminal labels carrying taxonomy info, or a whitelisted mapping file") which tells the agent when the tool is applicable. However, it names no alternatives and gives no explicit when-to-use vs check_monophyly guidance. Usage is implied via prerequisites rather than stated.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.