concatGenes: Concatenate Multiple Alignments

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

Description

This function concatenate multiple alignments

Usage

concatGenes(
  Genes,
  missing = c("?", "-"),
  write.dna = c(TRUE, FALSE),
  write.format = c("nexus", "phylip", "fasta", "tnt"),
  filename = NULL
)

Arguments

Genes	A list object with multiple alignments (DNAbin class)
missing	When a species or individual have no information for one or more genes, the absent gene(s) should be filled with "?" or "-". By default "?".
write.dna	Boolean, write the concatenate alignment in a file with predeterminate format. By deafault TRUE.
write.format	The format to write the concatenate alignment (only if write.dna == TRUE). Three options: 1. nexus (default), 2. phylip, 3. fasta or 4. tnt.
filename	The name of the output file (only if write.dna==TRUE).

Value

A concatenate alignment of DNAbin class

Author(s)

Omar Daniel Leon-Alvarado [e-mail]

See Also

multiMuscle completeGenes

Examples

library(alignTools)

data(Procyonidae)
head(Procyonidae, 5L)

genes <- multiGenBank(Procyonidae,TRUE,FALSE)

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

concat <- concatGenes(Genes=alignment, missing="?", write.dna=TRUE, write.format="phylip", filename="Concat_eg_output")

str(concat)

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