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jean — Molecular Biology & Genomics

draw_tree

Read-only

Draw a tree as an SVG figure — rectangular, slanted, circular or unrooted, as a phylogram or a cladogram, with tip names, branch support and a scale bar. The same layout the phylogeny panel draws with, so the figure and the panel place every node identically. Wire newick from build_tree or edit_tree.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
widthNofigure width. In px.
_filesNoThe project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
heightNofigure height. In px.
layoutNodrawing style; `unrooted` is the only honest one for a tree whose method inferred no root, because a rectangular drawing of it implies a root that was never inferred. Values: rectangular (Rectangular), slanted (Slanted), circular (Circular), unrooted (Unrooted).rectangular
newickYesthe tree to draw — wire `newick` from build_tree, or paste one.
supportNoprint each internal branch's support value where it carries one.
_subjectNoThe record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
font_sizeNotip-label size. In px. Advanced.
tip_labelsNoprint each tip's name, reserving the gutter they need.
length_unitNowhat the branch lengths MEAN, for the scale bar's caption. A tree read from a file carries no unit, so say what it is rather than letting the bar claim substitutions/site. Advanced.substitutions/site
min_supportNobelow this, a support value is not printed. Only applies when support is true. Advanced.
branch_lengthsNophylogram: horizontal distance IS evolutionary distance. Off draws a cladogram, which shows the topology alone — and then no scale bar is drawn, because the drawing is not to scale.
unrooted_methodNowhich unrooted algorithm places the nodes; equal daylight only rotates subtrees about their nodes, so it preserves every branch length. Only applies when layout is unrooted. Advanced.equal-angle

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
svgYesthe figure as an SVG string
widthYesfigure width in px
heightYesfigure height in px
tipCountYestips drawn
pixelsPerUnitYespx per unit of branch length in THIS drawing, or 0 when the drawing is not to scale and no bar was drawn

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.2/5.0
Behavior4/5

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

Annotations already declare the safety profile (readOnly, non-destructive, closed-world), so the bar is lower. The description adds genuinely new behavioral context: the figure reproduces the phylogeny panel's layout exactly, and the choice of phylogram vs cladogram governs whether a scale bar appears — details not derivable from the annotations alone.

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?

Three sentences, front-loaded with the verb+resource and output format, then the panel-parity value proposition, then the input wiring instruction. No filler; every clause carries information an agent can act on.

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?

With an output schema present, return values need not be explained, and the 100%-covered parameter schema handles the 13 inputs. The description covers what the tool produces (SVG figure) and its input source, leaving only minor gaps such as whether downstream tools consume the figure directly.

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

Parameters3/5

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

Schema description coverage is 100% and each of the 13 parameters is richly documented in the schema itself (layout enum rationale, branch_lengths/scale-bar coupling, min_support gating). The description only gestures at tip names, support and scale bar, adding little beyond what the schema already says, so the baseline 3 is appropriate.

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?

States a specific verb and resource (draw a tree as an SVG figure), then enumerates the layouts and the phylogram/cladogram distinction so the agent knows the exact output shape. It also names the sibling tools whose output feeds it (build_tree, edit_tree), separating it from neighbors like export_tree or transform_tree without needing the schema.

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

Usage Guidelines4/5

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

It tells the agent where the required `newick` comes from ('Wire newick from build_tree or edit_tree') and gives a real selection rule in the unrooted case (only honest layout when no root was inferred). There is no explicit when-not guidance or contrast against sibling export/comparison tools, so it stops short of a full 5.

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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