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

Annotations already declare readOnlyHint=true, destructiveHint=false, openWorldHint=false, so the safety profile is covered. The description adds real behavioral context beyond that: the all-ordered-pair N×N layout, that it ranks which members share material, and that reverse-complement plotting is a non-EMBOSS extension for spotting inversions. It does not restate the refusal thresholds for oversized sets, which live in the schema.

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?

Three sentences, front-loaded with the core action before the sibling differentiation and the input guidance. Every sentence contributes, though the third sentence's wiring hint overlaps with the schema and could be trimmed.

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?

With an output schema present, the description need not explain return values, and annotations plus 100% schema coverage carry the parameter and safety detail. The description supplies the remaining needed context: what a grid comparison is for and why it differs from the pairwise sibling. Complete enough for a 13-parameter tool.

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%, so the schema already documents all 13 parameters including `sequences`, `word_size`, and the guard rails. The description's guidance on `sequences` ('wire many upstream record/sequence outputs, or name library documents') largely repeats the schema text, adding little beyond it. Baseline 3 is appropriate.

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?

States a specific verb (all-against-all dot plot), the resource (a sequence SET), the underlying engine (EMBOSS polydot), and the output shape (N×N grid). It explicitly distinguishes itself from sibling `dot_plot` by scope: this one compares a whole family, that one exactly two.

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?

Names the alternative (`dot_plot`) and the condition that selects this tool over it ('Answers a different question from dot_plot, which compares exactly two'). It also tells the agent how to populate the required `sequences` argument, either by wiring upstream outputs or naming library documents.

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