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musharna

phylokit-mcp

by musharna
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Local

Engine capabilities and limits

capabilities
Read-onlyIdempotent

Identify the installed phylogenetic inference engine and IQ-TREE versions, and optionally list supported substitution models to confirm available analysis options.

Instructions

What this server can do, and the bounds it enforces.

engine_version is the installed piqtree version (e.g. "0.8.3"); iqtree_version is the IQ-TREE build inside it (e.g. "3.1.2").

Args: include_models: Include the full substitution-model list (long).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
include_modelsNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
engineYes
limitsYes
criteriaYes
aligner_errorYes
engine_versionYes
iqtree_versionYes
threads_pinnedYes
aligner_versionYes
support_thresholdsYes
substitution_modelsNo
n_substitution_modelsYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changedv0.6.0
    • addedOutput schema / properties / iqtree_version
      Added value: +{
+  "title": "Iqtree Version",
+  "type": "string"
+}
    • changedOutput schema / required
      Previous value: -[
-  "engine",
-  "engine_version",
-  "n_substitution_models",
-  "criteria",
-  "aligner_version",
-  "aligner_error",
-  "limits",
-  "support_thresholds",
-  "threads_pinned"
-]New value: +[
+  "engine",
+  "engine_version",
+  "iqtree_version",
+  "n_substitution_models",
+  "criteria",
+  "aligner_version",
+  "aligner_error",
+  "limits",
+  "support_thresholds",
+  "threads_pinned"
+]
  2. Changed4 schema fields changedv0.5.0
    • addedOutput schema / properties / aligner_error
      Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "title": "Aligner Error"
+}
    • addedOutput schema / properties / aligner_version
      Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "title": "Aligner Version"
+}
    • removedOutput schema / properties / substitution_models / default
      Removed value: -null
    • changedOutput schema / required
      Previous value: -[
-  "engine",
-  "engine_version",
-  "n_substitution_models",
-  "criteria",
-  "limits",
-  "support_thresholds",
-  "threads_pinned"
-]New value: +[
+  "engine",
+  "engine_version",
+  "n_substitution_models",
+  "criteria",
+  "aligner_version",
+  "aligner_error",
+  "limits",
+  "support_thresholds",
+  "threads_pinned"
+]
  3. First observedv0.1.0

TDQS

A3.9/5.0
Behavior4/5

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

Annotations already declare readOnlyHint, idempotentHint, and openWorldHint, and the description adds useful context about the version fields and the behavior of include_models. It also mentions enforced bounds, which goes beyond the structured annotations without contradicting them.

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?

The description is short, front-loaded with the tool's purpose, and each line serves a clear function. The 'Args:' header is slightly redundant with the schema, but there is no wasted prose.

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

Completeness5/5

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

Given the tool's simplicity, the existing output schema, and the annotations, the description is complete enough for correct invocation. It covers the version fields and the one behavioral toggle without needing to restate return formats.

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%, so the description must compensate for the single parameter. The line about include_models adds real meaning by clarifying that it controls whether the full substitution-model list is included and warns that the output is long.

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?

The description clearly conveys that the tool reports what the server can do and the limits it enforces, which distinguishes it from the phylogenetic analysis siblings. It lacks an explicit operative verb like 'returns' or 'lists', but the intent is unambiguous.

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 description implies this is an introspection capability for discovering server capabilities and limits, but it never explicitly says when to call it versus alternatives. It offers no direct 'use this when' guidance or comparison to sibling tools.

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

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