Whole Genome Hummingbird v15.4

Honest label — exploratory primitive. ML: deterministic sampled-pair distance likelihood hill-climbing with SPR topology and branch-length moves. MCMC: SPR topology moves with Metropolis-Hastings acceptance, accumulating posterior clade frequencies and averaged branch lengths. Large piles score a sampled subset of pairwise distances (Score pairs cap). Fast structure scouting. IUPAC ambiguity codes are accepted; RNA U is normalized to T; circular/viroid mode wraps k-mers across the FASTA cut point. Ambiguous symbols are reported as missing data and never counted as exact k-mers. Tamura-Nei 93 is available as an aligned/position-aware distance option, useful when records are homologous and comparable site-by-site. Not IQ-TREE, MrBayes, BEAST, RAxML, or MAFFT+Geneious. Fit sharpness (σ): this is a penalty sharpness parameter on the patristic distance regression, not a substitution-model sigma; it controls how steeply the scoring penalizes residuals after OLS rescaling of predicted to observed distances. SPR acceptance rate: a fraction of SPR proposals are topologically trivial no-ops (regraft at the original parent); the displayed acceptance rate is therefore a slight overestimate of true mixing efficiency. Tamura-Nei 93 base frequencies are computed from per-genome whole-sequence counts and averaged per pair, not solely from the pairwise aligned columns.