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phylogenetics

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UpdatedJuly 1, 2026 at 10:02

Phylogenetics & evolution (mirrors Claude Science's phylogenetics skill). MAFFT alignment + IQ-TREE tree building + selection/ancestral reconstruction, results shown next to the sequences that produced them. Use for multiple-sequence alignment, phylogenetic trees, selection analysis.

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JWM0203

JWM0203/Claude-Science-for-win

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Biological Scientists, All OtherLife, Physical, and Social Science Occupations·SOC 19-1029

SKILL.md

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name	phylogenetics
description	Phylogenetics & evolution (mirrors Claude Science's phylogenetics skill). MAFFT alignment + IQ-TREE tree building + selection/ancestral reconstruction, results shown next to the sequences that produced them. Use for multiple-sequence alignment, phylogenetic trees, selection analysis.

phylogenetics

Alignment MAFFT; trees IQ-TREE (or RAxML); sequence handling Biopython; sequence sources connectors/uniprot.py / ensembl.py.

Standard workflow

Collect sequences (inputs/, record source database + accession).
MAFFT alignment (record parameters) -> outputs/aln.fasta.
IQ-TREE: model selection + bootstrap >= 1000 -> outputs/tree.treefile.
Tree figure (figure-maker) + alignment view; branches correspond to input accessions.
When needed, dN/dS or ancestral reconstruction; state method and assumptions.

Hard rules

Record model, bootstrap, and random seed; every branch traces to an input sequence.

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