domains / families / science / tooluniverse-phylogenetics

tooluniverse-phylogenetics

separate

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/Nexus/Newick files, computing phylogenetic metrics, comparing taxa groups, or answering questions about alignments, trees, parsimony, or molecular evolution.

When to use

• 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 not to use

• Multiple sequence alignment generation
• Maximum Likelihood tree construction
• Bayesian phylogenetics
• Ancestral state reconstruction

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