Nextflow Modules
Showing module(s) with keyword "maximum likelihood"
| 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. |
| nf-core/cmaple | phylogeny phylogenetic tree maximum likelihood dna amino acid alignment tree reconstruction cmaple iqtree | Efficient phylogenetic tree reconstruction for sequences using the CMAPLE algorithm |
| nf-core/iqtree | phylogeny newick maximum likelihood | Produces a Newick format phylogeny from a multiple sequence alignment using the maximum likelihood algorithm. Capable of bacterial genome size alignments. |
| nf-core/raxmlng | phylogeny newick maximum likelihood | RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. |
| nf-core/raxmlng/search | phylogeny newick maximum likelihood model selection | Maximum-likelihood tree search with RAxML-NG, optionally combined with its integrated automatic model selection (MOOSE) |