tooluniverse-phylogenetics
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 tests, and batch analysis across gene families. Integrates with ToolUniverse for sequence retrieval (NCBI, UniProt, Ensembl) and tree annotation. Use when processing FASTA/PHYLIP/Nex
npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-phylogenetics --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Phylogenetics and Sequence Analysis 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. --- ## 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 -
- When to Use This Skill
- Core Principles
- Required Python Packages
- High-Level Workflow Decision Tree
- Quick Reference: Common Metrics
- Common Analysis Patterns (BixBench)
- Pattern 1: Single Metric Across Groups
- Pattern 2: Statistical Comparison
- Pattern 3: Filtering + Metric
- Pattern 4: Specific Gene Lookup
- Choosing Methods: When to Use What
- Alignment Methods
- Tree Building Methods
- Batch Processing
pip install phykit dendropy biopython pandas numpy scipy
What does the tooluniverse-phylogenetics skill do?
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 tests, and batch analysis across gene families. Integrates with ToolUniverse for sequence retrieval (NCBI, UniProt, Ensembl) and tree annotation. Use when processing FASTA/PHYLIP/Nex
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-phylogenetics --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.