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Scored across 21 tools
There is meaningful overlap between style_tree and apply_config (both apply a config plus operations and export Nexus), and the collapse_clade/collapse_group/collapse_rank trio requires careful reading to distinguish. run_figtreekit_cli also shadows nearly every other tool as an escape hatch. Descriptions do clarify intent, but an agent must parse them closely to avoid misselection.
Most tools follow a clear snake_case verb_noun pattern (get_environment, highlight_clade, collapse_rank, validate_tree). Minor deviations exist: taxonomy_completeness is noun-only, cross_validate is verb_verb, and setup_ vs set_ prefixes coexist. The overall convention is still predictable and readable.
21 tools falls in the borderline 16-25 band and feels heavy for a single MCP server, even for a broad tree-analysis domain. Several areas could be consolidated, such as the three collapse variants and style_tree/apply_config. Each tool has a plausible role, but the surface is larger than ideal.
Coverage is strong: setup/check, rendering, annotation add/clear, taxonomy analysis, monophyly checks, cross-validation, summarization, validation, export, styling and a full CLI escape hatch. Minor gaps in direct tree-shape operations (e.g., reroot, prune, rotate) can be worked around via run_figtreekit_cli. The lifecycle for core tree-styling and analysis workflows is well represented.