FigTreeKit-MCP

color_clade

Highlight a clade by coloring its MRCA branch or all descendant branches in a phylogenetic tree, using taxa and hex color.

Instructions

Color a clade's MRCA branch (all=false) or all descendant branches (all=true).

Args: colors: [{"taxa": ["A","B"], "color": "#2196F3", "all": false}].

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": "color_clade"
  }
}

Input Schema

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

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Oct 20, 2026

TDQS

C2.9/5.0

Behavior2/5

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

No annotations are provided, so the description carries the full behavioral burden. It implies a tree mutation but does not state what is modified, whether it needs an existing run/session, or what happens to prior colorings. Only the all-flag semantics are disclosed.

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 action and its branching behavior, followed by a compact example. Every sentence earns its place, though the Args example is terse and slightly cryptic for the colors structure.

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

Completeness2/5

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, but for a 4-parameter mutation tool with no annotations and 0% schema coverage, the description omits the meaning of run_name, tree_file, and tree_content. An agent cannot reliably call it without guessing these 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% and there are 4 parameters. The description documents the structure of the colors entry (taxa/color/all) but says nothing about run_name, tree_file, or tree_content, leaving half the parameters undocumented in both schema and description.

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 ('Color') and resource ('a clade's MRCA branch' / 'all descendant branches'), and clarifies the all=false vs all=true distinction. It does not explicitly differentiate from close siblings like highlight_clade or style_tree, so it falls short of a 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?

The all flag gives implied usage context (MRCA branch vs all descendants), but there is no guidance on when to use this versus highlight_clade or style_tree, nor any prerequisites. Usage is inferable but not stated.

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