phylogenetics

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

1. Collect sequences (inputs/, record source database + accession).
2. MAFFT alignment (record parameters) -> outputs/aln.fasta.
3. IQ-TREE: model selection + bootstrap >= 1000 -> outputs/tree.treefile.
4. Tree figure (figure-maker) + alignment view; branches correspond to input accessions.
5. 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.