read.multidna {apex}

Read multiple DNA alignments

Description

These functions read multiple DNA alignments and store the output in a multidna object. They are relying on ape's original functions read.dna and read.FASTA.

Usage

read.multidna(files, add.gaps = TRUE, ...)

read.multiFASTA(files, add.gaps = TRUE)

read.multiphyDat(files, add.gaps = TRUE, ...)

Arguments

files

a vector of characters indicating the paths to the files to read from.

add.gaps

a logical indicating if gap-only sequences should be added wherever sequences are missing; defaults to TRUE.

...

further arguments to be passed to the functions read.dna and read.FASTA.

Value

read.multidna and read.multiFASTA return an object of class multidna, read.multiphyDat returns an object of class multiphyDat.

Author(s)

Thibaut Jombart [e-mail]

Klaus Schliep [e-mail]

See Also

• read.dna

• read.FASTA

• read.phyDat

Examples

## get path to the files
files <- dir(system.file(package="apex"),patter="patr", full=TRUE)
files

## read files
x <- read.multiFASTA(files)
x
opar <- par(no.readonly=TRUE)
par(mfrow=c(2,2))
plot(x, row=FALSE)
par(opar)

y <- read.multiphyDat(files, format="fasta")
y