RADami (version 1.1-2)

rad2phy: Export a

Description

This function takes output from rad2mat and writes it to a phylip file, ready for analysis by RAxML or other software

Usage

rad2phy(pyDat, inds = row.names(pyDat), loci = dimnames(pyDat)[[2]],
        outfile = "pyMat.out.phy", padding = 50, verbose = FALSE,
        logfile ="rad2phy.log")

Arguments

pyDat

an object of class rad.mat

inds

individuals to include in the export

loci

loci to include in the export

outfile

file name for export

padding

total number of characters, including sequence title, to place before each sequence

verbose

whether to report on loci being written

logfile

name of logfile, which holds the names of loci in the phylip file written

Value

No value. This function is called for the side-effect of writing a phylip file

See Also

rad2mat, write.DNAStringSet