Nextflow Modules
Showing module(s) with keyword "phylogeny"
| Module | Keywords | Description |
|---|---|---|
| nf-core/cafe | gene phylogeny genomics | Analysis of gene family evolution |
| nf-core/clipkit | alignment trimming phylogeny | A multiple sequence alignment-trimming algorithm for accurate phylogenomic inference. |
| 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/epang/place | phylogeny phylogenetic placement sequences | phylogenetic placement of query sequences in a reference tree |
| nf-core/epang/split | phylogeny phylogenetic placement sequences | splits an alignment into reference and query parts |
| nf-core/fasttree | phylogeny newick alignment | Produces a Newick format phylogeny from a multiple sequence alignment. Capable of bacterial genome size alignments. |
| nf-core/gappa/examineassign | phylogeny phylogenetic placement classification taxonomy | assigns taxonomy to query sequences in phylogenetic placement output |
| nf-core/gappa/examinegraft | sort graft phylogeny | Grafts query sequences from phylogenetic placement on the reference tree |
| nf-core/gappa/examineheattree | phylogeny phylogenetic placement heattree visualisation | colours a phylogeny with placement densities |
| nf-core/gubbins | recombination alignment phylogeny | Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. |
| 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/muscle | msa multiple sequence alignment phylogeny | MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options are provided that give you the choice of optimizing accuracy, speed, or some compromise between the two |
| nf-core/orthofinder | genomics orthogroup orthologs gene duplication tree phylogeny | OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. |
| nf-core/rapidnj | phylogeny newick neighbour-joining | Produces a Newick format phylogeny from a multiple sequence alignment using a Neighbour-Joining 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/trimal | alignment trimming phylogeny | trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment. |