read: Reading Sequence Files

In ips: Interfaces to Phylogenetic Software in R

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)

Arguments

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

Value

An matrix (aligned sequences) or list (unaligned sequences) of class DNAbin or AAbin.

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)

ips documentation built on May 29, 2024, 4:39 a.m.