phylokit-mcp

Phylogenetic inference over MCP, driving IQ-TREE 2 through piqtree.

A topology without support is not a result. infer_tree always runs a bootstrap and always returns per-clade support. There is no flag to skip it.

5 tools, 62 tests against real IQ-TREE (no mocked engine), 10 mutation checks, and a real-process JSON-RPC handshake test.

Why the rule

A maximum-likelihood tree looks identical whether or not the data support it. Measured here, on alignments simulated from a known 7-taxon tree so the right answer is not in doubt:

sites	informative sites	recovered the true tree?	lowest clade support
300	51	yes, exactly	1.00
60	11	no — RF 2	0.57

At 60 sites the tree contains a clade (C,D,G) that does not exist and omits one that does (E,F,G). Both runs return a fully resolved Newick string of the same shape; nothing about the topology itself distinguishes them. The support values do — and the false clade is the lowest-supported one in the tree.

That is the entire argument for this server. Returning a bare tree returns a result the caller cannot evaluate.

What it reports that a Newick string cannot

• Conflicting clades — groupings the data support at ≥0.70 that are absent from the reported tree. A support-annotated Newick string has nowhere to attach these, so the standard format silently drops them.
• fraction_resolved — the share of clades clearing 0.70. The headline number, before any individual grouping is repeated as fact.
• Model runners-up with ΔAIC — not just a winner. On the 300-site alignment above, simulated under JC, the AIC winner is F81, with several models inside the conventional ±2 indistinguishability margin. A winner without its margin is a claim the numbers do not support.
• Length versus evidence — n_parsimony_informative alongside n_sites. A 10,000-site alignment of near-identical sequences supports nothing.

Tools

tool	what it does
infer_tree	ML tree plus bootstrap support, per clade. Never one without the other.
select_substitution_model	Ranks 100+ models with ΔAIC/AICc/BIC, and says when the criteria disagree.
compare_trees	Robinson–Foulds distance and the clades that differ. Compares splits, not strings.
simulate_alignment	Generates sequences along a tree you specify — the positive control.
capabilities	Engine version, 215 substitution models, enforced limits.

Install

pip install phylokit-mcp

piqtree ships prebuilt wheels, so there is no compiler, no R and no conda step — but it requires Python 3.12+, and so does this package.

Reproducibility, stated precisely

Measured, not assumed:

• Across fresh processes: exact. Three runs of an identical 30-replicate bootstrap returned byte-identical support.
• Within one long-lived process: not bit-exact. Passing the same rand_seed does not fully reset IQ-TREE's internal state — building the same tree three times gave call 1 == call 2 but call 3 different.

The practical size: over six repeated 50-replicate calls, three of four clades were bit-identical and one moved 0.02 — a single replicate flipping, well inside the bootstrap's own sampling error (~0.07 at 50 replicates). The topology and every conclusion were unchanged. This is reported in every response rather than papered over, because an MCP server is long-lived by design and that is exactly the condition which exposes it.

Threads are pinned to 1 before piqtree is imported: likelihood sums accumulate in thread-completion order, floating-point addition is not associative, and near-tied topologies can flip on the last bits.

Limitations

• Nucleotide alignments only. Protein and codon models are not exposed.
• Bootstrap only — no aLRT, no approximate Bayes, no UFBoot. Support is the nonparametric bootstrap (Felsenstein 1985), computed here rather than read back from IQ-TREE, because piqtree 0.8.3 runs bootstrap_replicates but does not expose the resulting values.
• Cost is linear in replicates. ~130 ms per replicate at 7 taxa / 300 sites, and it grows with taxon count. Capped at 200 taxa and 1000 replicates.
• It does not align sequences. Ragged input is refused, not guessed at.
• Unrooted trees. No rooting, no dating, no ancestral reconstruction.

Licence

GPL-2.0-only. The "only" is load-bearing: piqtree declares GPL-2.0-only, which is incompatible with GPL-3.0, so the distributed combination cannot be GPL-3. cogent3 is BSD and imposes nothing.