multiMuscle: Multiple Genes Alignment with MUSCLE

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

Description

This function is an extesion the muscle() function from ape. The x parameter is the only changed here, so, for more information about the other parameters, please see the documentation from ape.

Usage

multiMuscle(
  x = NULL,
  y,
  guide.tree,
  quiet = TRUE,
  original.ordering = TRUE,
  MoreArgs = "",
  write.dna = c("TRUE", "FALSE"),
  write.format = c("nexus", "phylip", "fasta", "tnt")
)

Arguments

x	A list object with multiple DNAbin objects
write.dna	Boolean, write each alignment as separate files in a predeterminate format. The file names will be the same as the x object names. By deafault 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).

Author(s)

Omar Daniel Leon-Alvarado [e-mail]

See Also

multiGenBank

Examples

library(alignTools)

data(Procyonidae)
head(Procyonidae, 5L)

genes <- multiGenBank(Procyonidae, TRUE, FALSE)

alignment <- multiMuscle(x=genes, write.dna=TRUE, write.format="phylip")

str(alignment) 
alignment$rag2

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