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Scored across 6 tools
Each tool targets a distinct stage or concern in the phylogenetic workflow: alignment, model selection, tree inference, tree comparison, simulation, and capabilities. There is no functional overlap; even the two 'tree' tools are clearly differentiated by purpose (compare topologies vs. infer from data).
Five of six tools follow the consistent verb_noun snake_case pattern (compare_trees, simulate_alignment, infer_tree, select_substitution_model, align_sequences). 'capabilities' breaks the pattern as a bare noun, but it is a standard introspection tool and the deviation is minor.
Six tools is well-scoped for a phylogenetics-focused server; each one earns its place and covers the core pipeline without redundancy or bloat. The count feels deliberately curated rather than padded.
The tool surface covers the complete typical workflow: align raw sequences, select a substitution model, infer a bootstrapped tree, compare trees, and simulate data for validation. The descriptions explicitly point to the next step in the pipeline, and there are no obvious dead ends or missing operations.