BioPython MCP Server

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

No annotations are provided, so the description carries the full burden of behavioral disclosure. It states the tool performs alignment and returns results, but lacks details on critical behaviors: it doesn't specify if it's read-only or destructive, mention performance constraints (e.g., sequence length limits), describe error handling, or explain the format of the 'Dictionary containing alignment results.' For a tool with no annotations, this is insufficient, though it does hint at external dependencies.

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 appropriately sized and well-structured, with clear sections for Args, Returns, and Note. It's front-loaded with the core purpose, and each sentence adds value: the first states the action, subsequent lines explain parameters and returns, and the note provides implementation context. There's no unnecessary verbosity, though the note could be more concise.

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 tool's moderate complexity (2 parameters, no annotations, but has an output schema), the description is partially complete. It covers the basic purpose and parameters but lacks usage guidelines, detailed behavioral context, and specifics on the output format (though the output schema might help). The note about external tools adds some context, but overall, it's adequate with clear gaps, especially for a tool with no annotations.

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 some semantics by explaining 'sequences' as a 'List of sequences to align' and 'algorithm' with a default value, but doesn't specify sequence formats (e.g., FASTA), valid algorithm options beyond 'clustalw', or constraints (e.g., minimum sequences). This provides basic meaning beyond the bare schema, but doesn't fully cover the gap, aligning with the baseline for partial compensation.

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 tool's purpose: 'Perform multiple sequence alignment.' It specifies the action ('Perform') and resource ('multiple sequence alignment'), which distinguishes it from siblings like 'pairwise_align' (for two sequences) or 'calculate_alignment_score' (for scoring rather than aligning). However, it doesn't explicitly differentiate from all siblings, such as 'find_motif' (which might involve alignment), so it's not a perfect 5.

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 provides no guidance on when to use this tool versus alternatives. It mentions that 'Full implementation would require external tools like MUSCLE or Clustal Omega,' but this is about implementation details, not usage context. There's no mention of when to choose this over 'pairwise_align' or other alignment-related tools, leaving the agent without practical usage instructions.

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