Run BEAST 2 Bayesian phylogenetic analysis

BEAST 2 is a Bayesian phylogenetics platform for estimating evolutionary relationships, divergence times, and associated uncertainty from aligned sequence data. It is used when a study needs posterior distributions, time calibration, or explicit uncertainty rather than a single best tree. Phylomena accepts an aligned nucleotide FASTA or Clustal file, along with optional partitions and calibration constraints, and builds the configuration required for the analysis. BEAST 2 generates a posterior sample of trees and model parameters; when selected, Phylomena runs TreeAnnotator to summarize these trees into a maximum clade credibility tree. For reproducibility, Phylomena records the input, analysis settings, random seed, executed commands, and resulting outputs.