readfiles: Read multiple DNA alignments

In apex: Phylogenetic Methods for Multiple Gene Data

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.

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

apex documentation built on April 14, 2020, 5:32 p.m.