phylokit-mcp
PYPI · PHYLOKIT-MCP · SCANNED SEP 20
Phylogenetic inference via IQ-TREE 2 — never returns a topology without its support
Available components
How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. How we score → Why this is hard to score →
Supply Chain Security49
- Malware scan not yet available for this package.Unverified
- Known CVEs were checked across the 50 of 52 dependencies we could resolve, so this covers what we could see, not the whole tree.Partial
- Runs hatchling.build at install time, a recognised native-build step with no shell scripting around it. View diagnostics → Pass
- Dependency health was assessed across the 50 of 52 dependencies we could resolve, so this covers what we could see, not the whole tree. View diagnostics → Partial
Provenance & Transparency35
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Provenance check failed: no build-provenance attestation is published. See how to fix → View diagnostics → Fail
- License check failed: no license is declared. See how to fix → Fail
- Actively maintained (last published 1 days ago).Pass
- Publishes a security disclosure policy (SECURITY.md).Pass
Schema Quality & AI Usability64
- AI-judged instruction clarity (good).Pass
- Context-footprint check failed: tool/resource definitions use about 1305 tokens (~217/item across 6 items; 6 tools + 0 resources), over budget; trim descriptions and params. See how to fix → Fail
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management87
- Stability observed for 26 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
Tool Coverage71
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 0% of tool parameters carry a description.Fail
- Structured output schemas are declared (100% of tools); any adoption earns full credit.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 6 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 7 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a current MCP spec version (2026-07-28).Pass
How do I install the phylokit-mcp server?
phylokit-mcp runs locally as a PyPI package, launched with uvx phylokit-mcp. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
pypi · phylokit-mcp
claude mcp add musharna-phylokit-mcp -- uvx phylokit-mcp
{
"mcpServers": {
"musharna-phylokit-mcp": {
"command": "uvx",
"args": [
"phylokit-mcp"
]
}
}
} {
"servers": {
"musharna-phylokit-mcp": {
"command": "uvx",
"args": [
"phylokit-mcp"
]
}
}
} codex mcp add musharna-phylokit-mcp -- uvx phylokit-mcp
{
"$schema": "https://opencode.ai/config.json",
"mcp": {
"musharna-phylokit-mcp": {
"type": "local",
"command": [
"uvx",
"phylokit-mcp"
],
"enabled": true
}
}
} openclaw mcp add musharna-phylokit-mcp --command uvx --arg phylokit-mcp
mcp_servers:
musharna-phylokit-mcp:
command: "uvx"
args: ["phylokit-mcp"] {
"McpServers": {
"musharna-phylokit-mcp": {
"Transport": "stdio",
"Command": "uvx",
"Arguments": [
"phylokit-mcp"
]
}
}
} assistant mcp add musharna-phylokit-mcp -t stdio -c uvx -a phylokit-mcp
{
"mcpServers": {
"musharna-phylokit-mcp": {
"command": "uvx",
"args": [
"phylokit-mcp"
]
}
}
} Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 19 Sept 26 −2
- Schema quality: 1085 → 1305 ▼ functional
- Schema quality: excellent → good functional
- Stability: pass → 0.83 functional
- Package version: 0.4.0 → 0.5.0 functional
- 18 Sept 26 0
- Stability: 0.97 → pass security
- 17 Sept 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 93 to 97. That category is still filling its 30-day observation window: 28 days of observed history at the previous scan, 29 at this one. The score rises as the window fills, whether or not the server changes.
- 15 Sept 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 87 to 90. That category is still filling its 30-day observation window: 26 days of observed history at the previous scan, 27 at this one. The score rises as the window fills, whether or not the server changes.
- 14 Sept 26 −15
- Malware scan: pass → unverified ▼ security
- 13 Sept 26 +16
- Malware scan: unverified → pass ▲ security
- 12 Sept 26 −3
- Stability: pass → 0.80 functional
- 11 Sept 26 0
- Stability: 0.97 → pass security
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 20 Sept 2026 · Analysed pypi/phylokit-mcp@0.5.0
Provenance No attestation
The registry publishes no build provenance for this version, so there is nothing to verify.
| Result | No attestation |
|---|---|
| Ecosystem | pypi |
Background: How many MCP packages publish verified provenance →
Install scripts 1 script
| Hook | Tier | Command |
|---|---|---|
| build_backend | allowlisted | hatchling.build |
Background: Why install scripts are a supply-chain risk →
Dependencies 50 packages
| Packages resolved | 50 |
|---|---|
| Stale | 1 |
| No linked repository | 2 |
| Tree resolution | Partial |
The dependency tree was only partially resolved, so these counts may be incomplete.
Background: SBOMs and build attestations, explained →
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
align_sequences Align sequences with MAFFT, ready for infer_tree ~164
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.
| Name | Type | Req | Description |
|---|---|---|---|
| fasta | string | yes | – |
| sequence_type | string | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| alignment | – | yes | – |
| engine | object | yes | – |
| fasta | string | yes | – |
| input_lengths | object | yes | – |
| ready_for_infer_tree | boolean | yes | – |
| sequence_type | string | yes | – |
| warnings | array | yes | – |
No examples provided.
capabilities Engine capabilities and limits ~43
What this server can do, and the bounds it enforces. Args: include_models: Include the full substitution-model list (long).
| Name | Type | Req | Description |
|---|---|---|---|
| include_models | boolean | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| aligner_error | – | yes | – |
| aligner_version | – | yes | – |
| criteria | array | yes | – |
| engine | string | yes | – |
| engine_version | string | yes | – |
| limits | object | yes | – |
| n_substitution_models | integer | yes | – |
| substitution_models | array | – | – |
| support_thresholds | object | yes | – |
| threads_pinned | boolean | yes | – |
No examples provided.
compare_trees Compare two tree topologies ~96
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.
| Name | Type | Req | Description |
|---|---|---|---|
| newick_a | string | yes | – |
| newick_b | string | yes | – |
| Name | Type | Req | Description |
|---|---|---|---|
| identical_topology | boolean | yes | – |
| n_shared_clades | integer | yes | – |
| normalised_robinson_foulds | – | yes | – |
| only_in_a | array | yes | – |
| only_in_b | array | yes | – |
| robinson_foulds | integer | yes | – |
| shared_taxa | integer | yes | – |
| warnings | array | yes | – |
No examples provided.
infer_tree Infer a phylogenetic tree with bootstrap support ~311
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 nucleotide sequences in FASTA. All sequences must be the same length — run `align_sequences` first if they are not. model: Substitution model, e.g. "JC", "HKY", "GTR+G". Run `select_model` first if you do not have a reason to prefer one. replicates: Bootstrap replicates (20-1000). Cost is roughly linear in this, so 100 is a reasonable default and 1000 is for a final answer. seed: Fixes both the resampling and the engine's search. sequence_type: "dna" (default) or "protein". DECLARED, never sniffed: an alignment of only A/C/G/T is a valid protein alignment too, so guessing would silently fit a nucleotide model to protein data. A protein alignment also needs a protein model — "LG+G" or "WAG", not the nucleotide default — so run select_substitution_model with the same sequence_type first.
| Name | Type | Req | Description |
|---|---|---|---|
| fasta | string | yes | – |
| model | string | – | – |
| replicates | integer | – | – |
| seed | integer | – | – |
| sequence_type | string | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| alignment | – | yes | – |
| branch_length_units | string | yes | – |
| engine | object | yes | – |
| log_likelihood | – | yes | – |
| model | string | yes | – |
| newick | string | yes | – |
| newick_with_support | string | yes | – |
| reproducibility | object | yes | – |
| support | – | yes | – |
| warnings | array | yes | – |
No examples provided.
select_substitution_model Rank substitution models, with the margin over the runners-up ~188
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 nucleotide sequences in FASTA. 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 models are not comparable.
| Name | Type | Req | Description |
|---|---|---|---|
| criterion | string | – | – |
| fasta | string | yes | – |
| seed | integer | – | – |
| sequence_type | string | – | – |
| top_n | integer | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| alignment | – | yes | – |
| best_by_criterion | object | yes | – |
| best_model | string | yes | – |
| criteria_agree | boolean | yes | – |
| criterion | string | yes | – |
| indistinguishable_from_best | array | yes | – |
| n_models_compared | integer | yes | – |
| ranking | array | yes | – |
| seed | integer | yes | – |
| warnings | array | yes | – |
No examples provided.
simulate_alignment Simulate an alignment from a known tree ~143
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 branch lengths. model: Substitution model to simulate under. length: Number of sites. seed: Fixes the simulation.
| Name | Type | Req | Description |
|---|---|---|---|
| length | integer | – | – |
| model | string | – | – |
| newick | string | yes | – |
| seed | integer | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| alignment | – | yes | – |
| fasta | string | yes | – |
| model | string | yes | – |
| seed | integer | yes | – |
| true_newick | string | yes | – |
| warnings | array | yes | – |
No examples provided.
What is the phylokit-mcp server?
phylokit-mcp is listed in the public MCP registry as io.github.musharna/phylokit-mcp. Phylogenetic inference via IQ-TREE 2, never returns a topology without its support. This page covers its PyPI package (phylokit-mcp).
Is the phylokit-mcp server safe to use?
phylokit-mcp scores 61 out of 100 on VerifyMCP. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.
What tools does the phylokit-mcp server expose?
phylokit-mcp exposes 6 tools: infer_tree, select_substitution_model, compare_trees, simulate_alignment, align_sequences, capabilities. Their descriptions and schemas cost roughly 945 tokens of context every time the server is loaded.
Is the phylokit-mcp server still maintained?
phylokit-mcp is still listed as active in the MCP registry. We last reached this channel on 20 September 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.