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

Annotations already declare this is a safe read-only operation, but the description adds meaningful behavioral detail: redundancy is computed as the highest percent identity to a row that is at least as long in ungapped residues, and thresholding keeps the longest representative. It does not describe the return structure, but an output schema exists.

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?

The definition is front-loaded with the core purpose and efficiently explains the redundancy rule. It is a dense single sentence, but every clause contributes to defining the operation and no wording is wasted.

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?

Given the complete input schema, read-only annotations, and an output schema, the description provides enough conceptual detail for correct invocation. It defines the algorithm and filtering outcome, though it could mention that rows should come from align_sequences as the schema notes.

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 all six parameters are already documented in the input schema. The description explains the threshold concept and the row-comparison logic, but adds little parameter-specific syntax beyond what the schema provides.

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?

The description uses a specific verb and resource: “Find the rows of an alignment that repeat another,” and defines what redundancy means in this context. It is clear enough to distinguish the operation from generic alignment tools, though it does not explicitly name sibling alternatives.

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?

The phrase “so filtering keeps the longest representative of each near-identical group” implies the tool is used to filter redundant alignment rows. However, it gives no explicit when-to-use guidance, prerequisites, or comparison with alternatives such as alignment_agreement or alignment_pca.

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