FigTreeKit-MCP

export_nexus

Convert Newick tree content into a base FigTree-compatible Nexus for structural export, optionally adding a TAXA block and naming the artifact; no styling applied.

Instructions

Low-level: load tree content and export a base FigTree-compatible Nexus (structural conversion only, Newick → Nexus; no styling).

Args: include_taxa_block: Emit a TAXA block (default true). run_name: Optional artifact base name.

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": "export_nexus"
  }
}

Input Schema

Name	Required	Description	Default
`run_name`	No
`tree_file`	No
`tree_content`	No
`include_taxa_block`	No

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Oct 20, 2026

TDQS

B3.2/5.0

Behavior3/5

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

With no annotations, the description carries the full burden, and it does disclose meaningful behavioral context: it is low-level, performs structural-only conversion with no styling applied, and include_taxa_block defaults to true. However, it says nothing about input source precedence (tree_file vs tree_content), permissions, or failure behavior.

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 one-line summary followed by a compact Args list; little waste. The embedded newline formatting is slightly awkward but the content earns its place.

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

Completeness3/5

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

An output schema exists so return values need not be explained, and the schema/annotation profile is light. Still, the ambiguity between tree_file and tree_content is a real gap for a converter with four optional inputs.

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

Parameters2/5

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

Schema description coverage is 0%, so the description must compensate, yet it documents only include_taxa_block and run_name. The two most important inputs, tree_file and tree_content, are entirely unexplained, leaving the agent unable to choose between a file path and inline content.

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 (load and export) and resource (base FigTree-compatible Nexus), and explicitly bounds scope with 'structural conversion only, Newick → Nexus; no styling'. This distinguishes it from styling siblings like style_tree. It stops short of naming a sibling alternative, so it lands at a clear 4 rather than 5.

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?

'Low-level' and 'structural conversion only ... no styling' imply when this tool applies (raw format conversion, not presentation), but no sibling alternative is named and no explicit when-not condition is given. Usage must be inferred.

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