completeGenes: Complete Alignments

In oleon12/alignTools: Easy download and manage GenBank data, and alignments for phylogenetics.

Description

Some softwares (e.g. RevBayes) for partitioned analysis required each gene in a separate file, but all files must have the same number of species. This function achive that task.

Usage

completeGenes(
  genes,
  missing = c("?", "-"),
  write.dna = c(TRUE, FALSE),
  write.format = c("nexus", "phylip", "fasta", "tnt")
)

Arguments

genes	A list object with multiple alignments (DNAbin class)
missing	When a species or individual have no information for a gene, the absent gene should be filled with "?" or "-". by default "?".
write.dna	Boolean, write on separate files each gene with the complete list of species or individuals. By default TRUE.
write.format	The format to write each alignment (only if write.dna==TRUE). Four options: 1. nexus (default), 2. phylip, 3. fasta or 4. tnt.

Value

A list object with multiple alignments (DNAbin class). All with the same number of species or individuals.

Author(s)

Omar Daniel Leon-Alvarado [e-mail]

See Also

concatGenes read.multiGenes

Examples

library(alignTools)

data(Procyonidae)
head(Procyonidae, 5L)

genes <- multiGenBank(Procyonidae,TRUE,FALSE)

alignment <- multiMuscle(genes, write.dna=FALSE)

complete <- completeGenes(genes=alignment, missing="?", write.dna=TRUE, write.format="fasta")

str(complete)

oleon12/alignTools documentation built on March 17, 2021, 4:57 p.m.