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tooluniverse-phylogenetics

维护者 FreedomIntelligence · 最近更新 2026年4月1日

tooluniverse-phylogenetics：Production-ready phylogenetics 、 sequence analysis skill ，用于 alignment processing，tree analysis，、 evolutionary metrics。 Computes treeness，RCV，treeness/RCV，parsimony informative sites，evolutionary rate，DVMC，tree length，alignment gap statistics，GC content，、 bootstrap support ，使用 PhyKIT，Biopython，、 DendroPy。

OpenClawNanoClaw分析处理复现实验tooluniverse-phylogenetics🏥 medical & clinicalmedical toolsproduction

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

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

维护者
FreedomIntelligence
许可
MIT
最近更新
2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

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

原始文档

SKILL.md 摘录

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

适用场景

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

不适用场景

  • Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。

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