rad2phy: Export a 'rad.mat' object to a phylip file

In andrew-hipp/RADami: Phylogenetic Analysis of RADseq Data

Export a rad.mat object to a phylip file

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

Author(s)

Andrew Hipp

See Also

rad2mat, write.DNAStringSet

andrew-hipp/RADami documentation built on Nov. 9, 2023, 5:40 p.m.