catGenes-package: Tools for combining individual DNA alignments for multigene...

In domingoscardoso/catGenes: Concatenating multiple DNA alignments and other phylogenetic features

Tools for combining individual DNA alignments for multigene analysis in phylogenetics and phylogenomics, and other phylogenetic features

Description

The catGenes package is under development and is intended to help researchers in phylogenetics and phylogenomics to build a fully concatenated or combined (non-interleaved) dataset by automatically comparing individual DNA alignments. Other features also involve mining DNA sequences or targeted loci from plastomes and mitochondrial genomes from GenBank, as well as plotting phylogenetic figures.

Details

The package's main functions catfullGenes and catmultGenes compare at least two individual DNA alignments with differing (or equal) number of sequences and creates equally-sized DNA alignments that are useful for concatenated phylogenetic or phylogenomic analyses. By using the functions writeNexus or writePhylip the user can write the catfullGenes- or catmultGenes-derived list of DNA alignments in NEXUS or PHYLIP format, respectively, which can serve for downstream model-based phylogenetic analyses in MrBayes, BEAST, RAxML or PAUP.

Another set of functions in this package allow the user to write a data.frame formatted DNA alignment (two-column-sized table including the taxon names and corresponding DNA sequence) as NEXUS, PHYLIP or FASTA formats: nexusdframe, phylipdframe, fastadframe. These are useful for readily writing each gene dataset from within the resulting list of compared gene datasets, after running the functions catfullGenes, catmultGenes or dropSeq.

For the most recent version of the catGenes, you are directed to package's page on github (http://www.github.com/domingoscardoso/catGenes).

Package:	catGenes
Type:	Package
Version:	0.10
Date:	2020-10-25

Author(s)

Domingos Cardoso
(email: [e-mail]; Website: https://biologia.ufba.br/domingos-benicio-oliveira-silva-cardoso)

Quezia Cavalcante
(email: [e-mail])

References

Cardoso, D. & Cavalcante, Q. (2024). catGenes: a new R package for combining multiple DNA alignments for multigene analysis in phylogenetics and phylogenomics.

See Also

Useful links:

• https://github.com/domingoscardoso/catGenes

domingoscardoso/catGenes documentation built on Jan. 5, 2025, 9:40 p.m.