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

Annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so the safety profile is covered. The description adds the identity of the statistical test, which helps interpret results, but says nothing about cost (permutation-based reanalysis), behavior with two loci, or failure modes for mismatched taxa.

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

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

A single front-loaded sentence stating the question and the method with a citation; no filler, nothing that could be cut.

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

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

An output schema exists and schema coverage is complete, so the short description is defensible. However, for a seven-parameter, nested-object statistical tool with close sibling tools, it leaves out the practical framing (when to choose it, what inputs are structurally required) that would let an agent call it confidently.

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

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

Schema description coverage is 100% and every parameter (loci, seed, alpha, correction, permutations, _files, _subject) is documented in the schema itself. The description adds no meaning beyond the schema, so the baseline 3 applies.

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

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

Names a specific analytical question (do some loci of a multi-locus alignment have a different history) and the exact method (incongruence length difference test, Farris et al. 1994). This is clearly distinguishable from tree-shape siblings like compare_trees or discover_gene_tree_discordance, though it never names an alternative explicitly.

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

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

Usage is only implied: an agent can infer it applies when a multi-locus alignment exists and the user asks about conflicting signal. There is no statement of prerequisites (minimum number of loci, identical taxon sets across files) or of when a different discordance tool would be more appropriate.

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