calculate_alignment_score

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

No annotations are provided, so the description must fully disclose behavior. It mentions using a substitution matrix and returning a dictionary, but lacks details on the expected format of alignment_str, error handling, or case sensitivity. This leaves ambiguity for the AI agent.

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 brief and front-loaded with the purpose. Every sentence adds value, and the Args/Returns structure is clear.

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 an output schema exists, the description need not detail return values. However, it omits critical details about the required format of alignment_str, which could cause errors. It is adequate but not fully complete.

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 0%, so the description must compensate. It adds meaning for both parameters: alignment_str is 'Aligned sequences (with gaps) as a formatted string' and matrix_name has a default value. However, it does not specify exact formatting or valid matrix names.

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 the verb 'Calculate' and the resource 'alignment score using a substitution matrix'. This distinguishes it from sibling tools that perform alignment creation (pairwise_align, multiple_sequence_alignment) or other analyses.

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 implies when to use the tool: to score an existing alignment. It does not explicitly say when not to use or mention alternatives, but the purpose is clear enough to differentiate from siblings.

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