phylokit-mcp

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Works with Claude Code, Codex, VS Code, Cursor, Windsurf, Claude Desktop. Read the repository before you give any tool access to your data.

npx agentmarket install connector/musharna-phylokit-mcp

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What this server can do and what it asks for, from its tool list, install config and code. Checked Oct 25, 2026.

Tools

1 read · 2 write · 0 delete · 4 not yet classified

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Python package

Tools (7)

Read from the source code; the running server may differ. Descriptions are the server’s own words; hidden characters are shown as [U+…].

• align_sequencesAlign sequences with MAFFT, ready for infer_tree

  Align unaligned sequences with MAFFT, ready for `infer_tree`. The returned `fasta` has every row the same length and can be passed to `infer_tree` or `select_substitution_model` unchanged. Each output row, with its gaps removed, is verified to equal the input sequence before it is returned. Args: fasta: UNALIGNED sequences in FASTA, 2-200 of them. Gap characters are refused: input that is already aligned does not need this tool. sequence_type: "dna" (default) or "protein". Declared, never sniffed, and passed to MAFFT explicitly so it does not guess either. fasta_p…

• capabilitiesEngine capabilities and limits

  What this server can do, and the bounds it enforces. `engine_version` is the installed piqtree version (e.g. "0.8.3"); `iqtree_version` is the IQ-TREE build inside it (e.g. "3.1.2"). Args: include_models: Include the full substitution-model list (long).

• compare_treesCompare two tree topologies

  Robinson-Foulds distance between two trees, and which clades differ. Compares SPLITS, not strings: the same topology has many valid Newick representations, so string equality answers a different question. Args: newick_a: First tree in Newick format. newick_b: Second tree in Newick format. trees_path: Instead of the two strings, the path of a file holding exactly two Newick trees, A then B.

• infer_treeInfer a phylogenetic tree with bootstrap support

  Build a maximum-likelihood tree and measure how well the data support it. Always bootstraps. There is deliberately no option to skip it: an unsupported topology is the failure mode this server exists to prevent. Args: fasta: Aligned sequences in FASTA, nucleotide or protein as declared by `sequence_type`. All sequences must be the same length — run `align_sequences` first if they are not. model: Substitution model, e.g. "JC", "HKY", "GTR+G" (or "LG+G" for protein). Run `select_substitution_model` first if you do not have a reason to prefer one. rep…

• map_positionsMap a residue to its alignment column and across sequences

  Map a residue to its alignment column, and the column to every sequence. Answers "which residue of B is in the same column as residue N of A" without counting by hand. Positions count residues from 1, gaps not counted; columns count from 1. At a gap, a row's position is null and `between` gives the residues either side. Args: aligned: true if the input is an alignment; false if unaligned, and it is aligned with MAFFT first, as `align_sequences` would. sequence: The sequence whose residue `position` is meant. position: A residue position in `sequence`. Give this or `column…

• select_substitution_modelRank substitution models, with the margin over the runners-up

  Compare substitution models and report how much the winner won by. A single model name reads as a finding. The ranking, the delta to the next model, and whether AIC/AICc/BIC agree are what make it one. Args: fasta: Aligned sequences in FASTA, nucleotide or protein as declared by `sequence_type`. criterion: "AIC", "AICc" or "BIC". BIC penalises parameters more heavily. seed: Fixes the engine's search. top_n: How many ranked models to return. sequence_type: "dna" (default) or "protein". Ranks within that molecule type's model set — nucleotide and protein mod…

• simulate_alignmentSimulate an alignment from a known tree

  Generate sequences along a tree you specify, so the true answer is known. This is the positive control for everything else here: infer a tree from the output and compare it back with `compare_trees`. If inference cannot recover a topology you generated from, the problem is the data or the settings, not the biology. Args: newick: The true tree, with a branch length on every edge. model: Substitution model to simulate under. A protein model ("LG", "WAG", ...) simulates protein; pass the output to `infer_tree` with sequence_type="protein". `alignment.moltype` says which …

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Last commit

Oct 23, 2026 (6 days ago)

Last release

Oct 20, 2026 (10 days ago)

Last package publish

Oct 20, 2026 (10 days ago)

From GitHub (fetched Oct 24, 2026) and the package registry.

Details

Registry name

io.github.musharna/phylokit-mcp

Version

0.7.0

Auth

No auth

Packages

pypi phylokit-mcp

License

GPL-2.0

Repository

github.com/musharna/phylokit-mcp

Website

github.com/musharna/phylokit-mcp

First seen

Oct 24, 2026

Last checked

Oct 24, 2026

Source

Official MCP Registrygithub-graphql