phangorn (version 0.0-5)

phyDat: Conversion amoung Sequence Formats

Description

These functions transform several DNA formats into the phyDat format. allSitePattern generates an alignment of all possible site patterns.

Usage

phyDat(data, type = "DNA", levels = NULL, return.index=FALSE, ...) 
## S3 method for class 'DNAbin':
as.phyDat(x, ...)
## S3 method for class 'phyDat':
as.character(x, ...)
## S3 method for class 'phyDat':
as.data.frame(x, ...)
allSitePattern(n, levels=c("a","c","g","t"), names=NULL)

Arguments

data

An object containing sequences.

x

An object containing sequences.

type

Type of sequences ("DNA", "AA" or "USER").

levels

Level atttributes.

return.index

If TRUE returns a index of the site patterns.

n

Number of sequences.

names

Names of sequences.

...

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.

Details

If type "USER" a vector has to be give to levels. For example c("a", "c", "g", "t", "-") would create a data object that can be used in phylogenetic analysis with gaps as fifth state. allSitePattern returns all possible site patternsis and can be usefull in simulation studies.

See Also

as.DNAbin, read.dna and read.nexus.data and the example of pmlMix for the use of allSitePattern

Examples

data(Laurasiatherian)
class(Laurasiatherian)
Laurasiatherian
# transform into old ape format
LauraChar <- as.character(Laurasiatherian)
# and back 
Laura <- phyDat(LauraChar, return.index=TRUE)
all.equal(Laurasiatherian, Laura)
allSitePattern(5)