Nextflow Modules
Showing module(s) with keyword "codon models"
| Module | Keywords | Description |
|---|---|---|
| nf-core/bppsuite/bppml | branch length estimation maximum likelihood substitution models site-specific rate distributions nucleotide models codon models protein models | 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. |