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musharna
by musharna

Compare two tree topologies

compare_trees
Read-onlyIdempotent

Compute Robinson-Foulds distance between two phylogenetic trees and identify which clades differ.

Instructions

Robinson-Foulds distance between two trees, and which clades differ.

Compares SPLITS, not strings: the same topology has many valid Newick representations, so string equality answers a different question.

Args: newick_a: First tree in Newick format. newick_b: Second tree in Newick format.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
newick_aYes
newick_bYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
warningsYes
only_in_aYes
only_in_bYes
shared_taxaYes
n_shared_cladesYes
robinson_fouldsYes
identical_topologyYes
normalised_robinson_fouldsYes
Behavior3/5

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

Annotations already declare readOnlyHint and idempotentHint true, so the description adds only the nuance that it compares splits. No contradictions, but minimal extra behavioral disclosure.

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

Conciseness5/5

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

Three concise lines plus Args, no redundancy. Every sentence adds value; front-loaded with purpose.

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?

Tool is simple with two params and has an output schema. Description covers concept, input format, and key distinction (split vs string). Complete for the complexity.

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 has 0% description coverage, but the description's Args section adds meaning: 'First tree in Newick format' and 'Second tree in Newick format'. This compensates well, though not exhaustive.

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

Purpose5/5

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

Clearly states it computes Robinson-Foulds distance and identifies differing clades, distinguishing it from string comparison. Specific verb+resource with unique focus.

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

Usage Guidelines4/5

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

Explicitly compares splits not strings, hinting that string equality is a different task. Sibling tools like infer_tree are distinct, so no confusion. Slightly lacking explicit when-not or alternatives.

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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