Align sequences with MAFFT, ready for infer_tree

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

The description adds substantial behavior beyond the annotations. It discloses that each output row is verified to equal the input after gap removal, that sequence_type is declared and never sniffed, and that gap characters are refused. These are meaningful constraints not present in the readOnlyHint and idempotentHint annotations, and no contradiction 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 description is concise yet information-dense. The opening line states the purpose, the second paragraph covers output guarantees, and the Args section clarifies each parameter. Every sentence adds value; there is no filler or repetition.

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?

The description is complete for this tool. It covers input constraints, output behavior, parameter semantics, and how the output integrates with sibling tools. Since an output schema exists, the description need not enumerate return fields, and it does not. Nothing an agent needs to invoke it correctly is missing.

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?

With 0% schema coverage, the description fully compensates. It explains the fasta parameter: unaligned sequences, 2-200 count, and refusal of gap characters. For sequence_type, it specifies 'dna' or 'protein' and that it is declared and passed explicitly to MAFFT, adding critical semantics beyond the schema's bare type/default.

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 clearly states a specific verb and resource: 'Align unaligned sequences with MAFFT'. It distinguishes itself from siblings by specifying the input must be unaligned and that the output is ready for infer_tree. It also explicitly notes that already-aligned input does not need this tool, separating it from any alignment-related 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 description explicitly states when to use the tool (unaligned sequences, 2-200) and when not to use it (input with gap characters is refused, and already-aligned input does not need this tool). It also names downstream tools (infer_tree, select_substitution_model) that can consume the output unchanged, giving clear routing context.

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