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tooluniverse-phylogenetics

Maintainer FreedomIntelligence · Last updated April 1, 2026

Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics. Computes treeness, RCV, treeness/RCV, parsimony informative sites, evolutionary rate, DVMC, tree length, alignment gap statistics, GC content, and bootstrap support using PhyKIT, Biopython, and DendroPy. Performs NJ/UPGMA/parsimony tree construction, Robinson-Foulds distance, Mann-Whitney U t….

OpenClawNanoClawAnalysisReproductiontooluniverse-phylogenetics🏥 medical & clinicalmedical toolsproduction

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/tooluniverse-phylogenetics

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Comprehensive phylogenetics and sequence analysis using PhyKIT, Biopython, and DendroPy. Designed for bioinformatics questions about multiple sequence alignments, phylogenetic trees, parsimony, molecular evolution, and comparative genomics.
  • IMPORTANT: This skill handles complex phylogenetic workflows. Most implementation details have been moved to references/ for progressive disclosure. This document focuses on high-level decision-making and workflow orchestration.
  • import numpy as np import pandas as pd from scipy import stats from Bio import AlignIO, Phylo, SeqIO from Bio.Phylo.TreeConstruction import DistanceCalculator, DistanceTreeConstructor.

Source Doc

Excerpt From SKILL.md

When to Use This Skill

Apply when users:

  • Have FASTA alignment files and ask about parsimony informative sites, gaps, or alignment quality
  • Have Newick tree files and ask about treeness, tree length, evolutionary rate, or DVMC
  • Ask about treeness/RCV, RCV, or relative composition variability
  • Need to compare phylogenetic metrics between groups (fungi vs animals, etc.)
  • Ask about PhyKIT functions (treeness, rcv, dvmc, evo_rate, parsimony_informative, tree_length)
  • Have gene family data with paired alignments and trees
  • Need Mann-Whitney U tests or other statistical comparisons of phylogenetic metrics
  • Ask about bootstrap support, branch lengths, or tree topology
  • Need to build trees (NJ, UPGMA, parsimony) from alignments
  • Ask about Robinson-Foulds distance or tree comparison

BixBench Coverage: 33 questions across 8 projects (bix-4, bix-11, bix-12, bix-25, bix-35, bix-38, bix-45, bix-60)

NOT for (use other skills instead):

  • Multiple sequence alignment generation → Use external tools (MUSCLE, MAFFT, ClustalW)
  • Maximum Likelihood tree construction → Use IQ-TREE, RAxML, or PhyML
  • Bayesian phylogenetics → Use MrBayes or BEAST
  • Ancestral state reconstruction → Use separate tools

Core Principles

  1. Data-first approach - Discover and validate all input files (alignments, trees) before any analysis
  2. PhyKIT-compatible - Use PhyKIT functions for treeness, RCV, DVMC, parsimony, evolutionary rate (matches BixBench expected outputs)
  3. Format-flexible - Support FASTA, PHYLIP, Nexus, Newick, and auto-detect formats
  4. Batch processing - Process hundreds of gene alignments/trees in a single analysis
  5. Statistical rigor - Mann-Whitney U, medians, percentiles, standard deviations with scipy.stats
  6. Precision awareness - Match rounding to 4 decimal places (PhyKIT default) or as requested
  7. Group comparison - Compare metrics between taxa groups (e.g., fungi vs animals)
  8. Question-driven - Parse exactly what is asked and return the specific number/statistic

Use cases

  • Have FASTA alignment files and ask about parsimony informative sites, gaps, or alignment quality.
  • Have Newick tree files and ask about treeness, tree length, evolutionary rate, or DVMC.
  • Ask about treeness/RCV, RCV, or relative composition variability.
  • Need to compare phylogenetic metrics between groups (fungi vs animals, etc.).

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

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