Description
Bio++ Maximum Likelihood Computation (bppml) is a command-line tool within the Bio++ suite designed for maximum likelihood estimation of evolutionary parameters on phylogenetic trees. It estimates branch lengths, substitution model parameters (such as $d_N/d_S$ ratios, transition/transversion ratios, or amino acid replacement matrices), site-specific rate distributions, and equilibrium frequencies for nucleotide, codon, or protein alignments under defined phylogenetic models.
Tools
bppsuite Documentation
BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analysis.
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