Analyze monophyly of all groups at a given taxonomic rank.

Equivalent to figtreekit --analyze-taxonomy RANK. Requires terminal labels carrying taxonomy info, or a whitelisted mapping file.

Args: tree_content: Newick/Nexus content. tree_file: Path to a tree file inside an allowed read root. rank: Taxonomic rank to analyze (domain..species). taxonomy_mapping_file: Optional CSV/TSV mapping (whitelisted). taxonomy_levels: prefix:rank list. group_size_min: Only report groups with at least this many taxa.

Apply a FigTree JSON config (figtree-block keys) plus an ordered operations list and export Nexus. Leaner than style_tree for agent-driven advanced tweaks.

All accepted parameters are validated before execution (collapse_style, multi_tree, auto_color_rank/collapse_rank and every operation field); the execution order is annotations → auto-color/collapse-rank → collapse operations, matching the CLI.

Args: config: Any figtree-block key → value mapping (dot-separated keys). operations: Ordered clade operations (same schema as style_tree). taxonomy_levels: Custom rank prefixes (prefix:rank,...); active during both loading and taxonomy analysis. seed: Reproducible tree selection for multi_tree="random".

Check Java 8+ and the figtree_patched.jar; return actionable hints.

Args: jar_path: Optional explicit JAR path to check instead of auto-detection.

Check whether one or more taxonomic groups are monophyletic.

Supports special identifiers LUCA / LACA / LBCA / root, and exact taxon lists. strict=True raises monophyly_error as soon as any group is not monophyletic.

Args: tree_content: Newick/Nexus content. tree_file: Path to a tree file inside an allowed read root. groups: List of group names (str) or exact taxon lists (list[str]). taxonomy_levels: prefix:rank list (e.g. "d:domain,p:phylum"). strict: Fail on any non-monophyletic group.

Clear highlight and collapse annotations, including embedded ones.

Both pending annotations and [&!hilight=...] / [&!collapse=...] comments already present in the input tree text are removed before the tree is loaded/exported. Colors and fonts are intentionally NOT part of this tool (use color_clade / set_clade_font to manage them).

Args: clear_hilights: Clear background highlights (default true). clear_collapses: Clear collapses/cartoons (default true). strip_annotations: Also strip generic [&...] annotations from the text. Nexus root markers [&R] / [&U] are preserved so rooting is unchanged.

Collapse clades by exact taxon names into collapse (triangle+label) or cartoon style.

Args: collapses: [{"taxa": ["A","B","C"], "label": "Clade1", "collapse_type": "collapse|cartoon"}].

Collapse clades by taxonomic group name with a monophyly pre-check (supports LUCA / LACA / LBCA / root).

A group whose lookup fails (unknown name / unresolvable taxonomy) is recorded as a per-group skipped entry and never aborts the whole request; strict=True converts that failure into monophyly_error.

Args: groups: [{"group": "Cyanobacteriota", "label": "...", "collapse_type": "collapse"}]. strict: Fail with monophyly_error on a non-monophyletic group. taxonomy_levels: Custom rank prefixes (prefix:rank,...). taxonomy_mapping_file: Optional taxonomy mapping table (whitelisted), for trees whose taxonomy is not embedded in tip labels.

Collapse all monophyletic groups at a rank (optionally auto-coloring at a rank first) — reproduces figtreekit --collapse-rank.

Args: rank: Rank to collapse (class, phylum, ...). collapse_style: collapse | cartoon. auto_color_rank: Rank for the pre-collapse palette coloring (defaults to phylum, matching the CLI). strict: Fail when a monophyletic group cannot be collapsed. taxonomy_mapping_file: Optional taxonomy mapping table (whitelisted), for trees whose taxonomy is not embedded in tip labels.

Color a clade's MRCA branch (all=false) or all descendant branches (all=true).

Args: colors: [{"taxa": ["A","B"], "color": "#2196F3", "all": false}].

Cross-validate tree tip labels against sequence IDs (FASTA/FASTQ).

Args: tree_content: Newick/Nexus content. tree_file: Path to a tree file inside an allowed read root. sequences_file: Path to the sequence file (must be whitelisted). strict: Raise validation_failed on any mismatch (default true). low_memory: Accepted for figtreekit parity; IDs are always read lazily.

Low-level: load tree content and export a base FigTree-compatible Nexus (structural conversion only, Newick → Nexus; no styling).

Args: include_taxa_block: Emit a TAXA block (default true). run_name: Optional artifact base name.

Report the FigTreeKit-MCP runtime environment.

Returns versions of figtreekit / biopython / python / the MCP SDK, Java and figtree_patched.jar availability, the workspace root, and the allowed read-only roots.

Add FigTree hilight annotations (background bands) to one or more clades.

Args: highlights: [{"taxa": ["A","B"], "color": "#804548", "width": 1.0, "offset": 0}] entries. offset must be an integer (the CLI parses --highlight offsets with int()). clear_existing: Clear existing highlights before applying — including [&!hilight=...] comments already embedded in the tree text (not just pending annotations).

Render a Nexus file (or tree content) to PNG/PDF/SVG/JPEG via the patched FigTree JAR; returns paths plus an optional base64 data URI preview. Applies background/foreground/label colour post-processing for raster formats.

Args: nexus_file: Path to a Nexus file (whitelisted; takes precedence). tree_content: Newick/Nexus content rendered through a base export. format: PNG|PDF|SVG|JPEG (default PNG). width: Image width in pixels. height: Image height in pixels. background_color: #RRGGBB background (raster post-process). foreground_color: #RRGGBB foreground (raster post-process). label_color: #RRGGBB protected label colour. jar_path: Explicit figtree_patched.jar path (default: app config / auto-detection). timeout: Max seconds for the JVM render call (default: app.render_timeout, normally 180). run_name: Optional artifact base name.

Run the figtreekit CLI with arbitrary argv (full CLI coverage; no shell). Outputs are redirected into the run directory; each rewrite is disclosed in rewrites.

Args: argv: The figtreekit arguments as an array. Use <input> as a placeholder consumed by tree_content / input_file. tree_content: If provided, written as run_dir/input.tre and replaces <input> in argv. input_file: Or a whitelisted file reference (same placeholder rule). timeout: Max execution seconds (default 300). capture_tail_bytes: Max bytes of stdout/stderr kept (default 64 KiB).

Set font name/style/size for a clade's tip labels.

Args: fonts: [{"taxa": ["A"], "font_name": "Arial", "font_style": 1, "font_size": 14}]; font_style 0 plain / 1 bold / 2 italic / 3 bold-italic.

Download (or use given jar) and compile the patched FigTree JAR.

Args: jar_path: Optional existing JAR to use (whitelisted; no compile). check_only: Only check dependencies (no download/compile). verbose: Print step-by-step setup progress.

Style a tree with the full FigTreeKit parameter surface and export a FigTree-compatible Nexus file. Returns the file, an equivalent cli_command and a config_json for byte-for-byte reproducibility, plus per-operation records.

Execution order mirrors the CLI: plain clade annotations (highlight / color / font / clear) → taxonomy auto-color / collapse-rank → collapse operations. --color-all is a global CLI switch, so mixing color and color_all operations cannot be represented exactly on the command line (the command colors every listed clade).

Multi-tree files: multi_tree="first"|"last"|"random" style one tree and export only that tree (CLI parity); pass seed to make random reproducible. split/all cannot be reproduced by a single MCP artifact (the CLI writes one file per tree), so the selected tree is styled while all trees are preserved, and an explicit warnings entry is returned.

Args: See the mapped parameter table in docs/tools_reference_EN.md; every argument is optional (unspecified = figtreekit default).

Parse and summarize a tree: format, counts, root state, branch stats.

Never fails on validation issues (use validate_tree for that); a multi-tree file without an explicit selection yields a multi_tree_hint instead of an error.

Args: tree_content: Newick/Nexus content. tree_file: Path to a tree file inside an allowed read root. include_tip_labels: Include the tip-label preview. tip_labels_limit: Max number of preview labels (1..10000). multi_tree: first|last|random|split|all selection for multi-tree Nexus. tree_index: 0-based index into a multi-tree Nexus.

Report taxonomy completeness per rank; list complete/incomplete/missing tips.

Equivalent to figtreekit --check-taxonomy. Lists are truncated to the first 200 entries; totals are always returned.

Args: tree_content: Newick/Nexus content. tree_file: Path to a tree file inside an allowed read root. taxonomy_mapping_file: Optional CSV/TSV mapping (whitelisted). taxonomy_levels: prefix:rank list.

Deep-validate a Newick/Nexus tree or FASTA/FASTQ sequence file.

Returns structured errors, warnings, format and counts. Semantics match figtreekit --validate but no persistent artifact is written.

Args: tree_content: Newick/Nexus/FASTA/FASTQ content (direct paste). tree_file: Path to a tree/sequence file inside an allowed read root. mol_type: Expected alphabet for sequences (DNA|RNA|protein). skip_length_check: Skip alignment-length consistency check (FASTA).