read.fas: Read DNA Sequences
In fmichonneau/phyloch: Tools for phylogenetics and taxonomy

Description Usage Arguments Value Author(s) References See Also Examples

This functions parse DNA sequences in FASTA, PHILIP, and NEXUS formatted files.

read.fas(x, text)

read.nex(x)

read.phy(x)

`x`	a character string, giving the file name.
`text`	a character string in FASTA format.

An object of class DNAbin and of mode matrix if all sequences are of same length or matrix if they are not.

Christoph Heibl

Maddison, D.R., D.L. Swofford, and W.P. Maddison. 1997. NEXUS: an extensible file format for systematic information. Syst. Biol. 46: 590-621.

mafft and prank for sequence alignment, gblocks and aliscore for quality check and cleaning of sequence alignments, c.genes for concatenation of sequence alignments.

# sequence data:
data(woodmouse)

# write sequences files
write.fas(woodmouse, "phyloch.fas")
write.phy(woodmouse, "phyloch.phy")
write.nex(woodmouse, "phyloch.nex")

# read sequence files
fas <- read.fas("phyloch.fas")
phy <- read.phy("phyloch.phy")
nex <- read.nex("phyloch.nex")

# remove sequence files
unlink("phyloch.*")