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tooluniverse-phylogenetics

Compute phylogenetic tree and alignment metrics from FASTA and Newick files using PhyKIT.

1.7k|254|Updated Mar 3, 2025
Search Tags:#BUSCO#comparative genomics#phylogenetics#mann-whitney#tree analysis#sequence alignment#phykit
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-phylogenetics
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-phylogenetics
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-phylogenetics
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-phylogenetics

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires phykit, biopython, dendropy, numpy, pandas, scipy, and includes scripts (resource) and references (resource) components.

What problem does it solve?

Phylogenetic analysis requires computing dozens of tree and alignment statistics (treeness, RCV, DVMC, parsimony-informative sites, saturation, long-branch scores) across hundreds of ortholog files, then running group comparisons like Mann-Whitney U tests. Doing this manually with PhyKIT per file is slow, error-prone, and easy to get wrong by parsing the wrong output column or processing only a sample of genes.

Core Features & Use Cases

  • Batch PhyKIT metrics: Compute treeness, saturation, DVMC, evolutionary rate, tree length, long-branch score, patristic distances, RCV, gap percentage, and parsimony-informative sites across entire directories of alignments and trees.
  • BUSCO scogs pipelines: Bundled scripts extract pre-computed alignments and trees from scogs_animals.zip / scogs_fungi.zip, apply single-copy ortholog intersection rules, and emit per-group summaries plus Mann-Whitney U statistics in one pass.
  • De novo alignment and tree building: Align raw sequences with Clustal Omega, MUSCLE, or MAFFT via EBI_msa_align, then build neighbour-joining or UPGMA trees with EBI_build_phylogenetic_tree.
  • Use Case: Given a data folder of fungal and animal ortholog trees, answer "what is the median DVMC for fungi and the Mann-Whitney U statistic comparing fungi vs animals" with a single script invocation.

Quick Start

Ask the agent to compute the median treeness across all tree files in your data folder and compare the fungi and animals groups with a Mann-Whitney U test.

Frequently Asked Questions about tooluniverse-phylogenetics

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I compute treeness across hundreds of gene trees?▼

Use the phykit_batch_analysis tool or the bundled phykit_batch.py script pointed at the directory of .treefile files. It runs PhyKIT treeness on every file and returns mean, median, min, and max, avoiding manual per-file loops.

How to compare fungi vs animals phylogenetic metrics with Mann-Whitney U?▼

Run scogs_paired_compare.py with the data folder containing scogs_animals.zip and scogs_fungi.zip and choose a metric. It computes per-ortholog values for both groups and emits two-sided Mann-Whitney U statistics and p-values in one pass.

Can this skill build maximum-likelihood trees with IQ-TREE or RAxML?▼

No. Tree construction is limited to distance-based neighbour-joining and UPGMA via EBI_build_phylogenetic_tree. For maximum-likelihood or Bayesian phylogenies, use dedicated tools or the pre-computed treefiles shipped in scogs archives.

Why does phykit parsimony_informative return no output?▼

parsimony_informative is not a valid PhyKIT CLI subcommand; the correct name is parsimony_informative_sites (alias pis). The bundled scripts translate the name automatically and parse the percentage from column three of the output.

What Python packages are required for phylogenetic analysis here?▼

The skill requires phykit, biopython, dendropy, numpy, pandas, and scipy. All computation runs locally, so no API keys are needed unless you optionally use ToolUniverse database integrations.

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