phangorn (version 0.0-2)

phyDat: Conversion amoung Sequence Formats

Description

These functions transform several DNA formats into the phyDat format.

Usage

phyDat(data, levels, return.index=FALSE)
phyDat.DNA(data, return.index=FALSE) 
## S3 method for class 'DNAbin':
as.phyDat(data, ...)
## S3 method for class 'phyDat':
as.character(x, ...)
## S3 method for class 'phyDat':
as.data.frame(x, ...)

Arguments

data

An object containing sequences.

levels

Level atttributes.

return.index

If TRUE returns a index of the site patterns.

x

An object of class phyDat.

...

further arguments passed to or from other methods.

Value

• The functions return an object of class phyDat. You may import data with read.dna or read.nexus.data.

See Also

as.DNAbin, read.dna and read.nexus.data

Examples

data(Laurasiatherian)
class(Laurasiatherian)
Laurasiatherian
# transform into old ape format
LauraChar <- as.character(Laurasiatherian)
# and back 
Laura <- phyDat.DNA(LauraChar, return.index=TRUE)
all.equal(Laurasiatherian, Laura)