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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

The catGenes package 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.

Installation

Developmental using devtools

devtools::install_github("domingoscardoso/catGenes")
library(catGenes)

Standard format for input DNA alignments

Before loading the DNA alignments to run catGenes functions, make sure the DNA aligments have the species names format as following:

(i) Underscores separate the genus and species name from the collector+number+genbank accession

Genus_species_everythingelse

(ii) so... no problem if the genus name is abbreviated

G_species_everythingelse

Usage

path <- system.file("DNAlignments", package = "catGenes")

ITS <- read.nexus.data(paste0(path, "/Gaya_ITS.nex"))

domingoscardoso/catGenes documentation built on March 14, 2024, 9:21 p.m.