ips (version 0.0.13)

read: Reading Sequence Files

Description

Read DNA and amino acid sequences from FASTA, PHILIP, and NEXUS formatted files.

Usage

read.fas(x, text)
read.nex(x)
read.phy(x)

Value

An matrix (aligned sequences) or list (unaligned sequences) of class

DNAbin or AAbin.

Arguments

x

A character string, giving the file name.

text

A character string in FASTA format.

References

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

See Also

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

Examples

## bark beetle COX1 sequences
data(ips.cox1)
## create temporary file names
format <- c(".fas", ".phy", ".nex")
fn <- sapply(format, tempfile, 
             pattern = "ips", tmpdir = tempdir())
## write sequences files
write.fas(ips.cox1, fn[".fas"])
write.phy(ips.cox1, fn[".phy"])
write.nex(ips.cox1, fn[".nex"])
## read sequence files
fas <- read.fas(fn[".fas"])
phy <- read.phy(fn[".phy"])
nex <- read.nex(fn[".nex"])
## remove sequence files
unlink(fn)