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kmaneesh

BioPython MCP Server

by kmaneesh

draw_tree

Convert a Newick format tree into a visual representation (ASCII text) for phylogenetic analysis. Specify the tree in Newick string and optionally choose output format to get a tree diagram.

Instructions

Draw a phylogenetic tree from Newick format.

Args: tree_newick: Tree in Newick format output_format: Output format - 'ascii' for text representation (default: 'ascii')

Returns: Dictionary containing tree visualization

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
tree_newickYes
output_formatNoascii

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior3/5

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

No annotations are provided, so the description must cover behavior. It mentions the return type but does not disclose any side effects, error handling, or constraints, which is acceptable for a simple drawing tool but not thorough.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is extremely concise: a one-sentence purpose, then a bullet-point parameter list, and a returns line. No wasted words, and all relevant information is included.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool has only two parameters, no annotations, and an output schema exists, the description is fairly complete. It covers inputs and return type, but lacks examples or error handling details, which are minor omissions.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The schema has 0% description coverage, so the description must add meaning. It explains both parameters: tree_newick is the tree in Newick format, output_format has a default of 'ascii' for text representation, adding significant value beyond the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool draws a phylogenetic tree from Newick format, with a specific verb and resource. It distinguishes from sibling tools like build_phylogenetic_tree, which likely builds trees from other data.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Usage is implied: use when you have a Newick string. However, no explicit when-to-use or alternatives are mentioned, leaving some ambiguity.

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

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