Build an auditable protein or nucleotide gene tree from an accession, explicitly declared local sequence, or gene, protein, or feature name plus source organism. Use when an agent must choose an environment-appropriate route; resolve metadata and exact NCBI TaxIDs; classify gene-family conservation at an explicit taxonomic scope; curate references and outgroups; align proteins, noncoding DNA or RNA, or clean CDS through a protein-guided codon-preserving route; run FastTree or IQ-TREE2; generate iTOL or ggtree/ggplot2 outputs; or compare a gene tree with current literature. Require review gates before reference selection, alignment choice, and tree inference.
