phangorn (version 0.99-4)

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=TRUE, ...) 
read.phyDat(file, format="phylip", type="DNA", ...)
write.phyDat(x, file, format="phylip",...)
## S3 method for class 'DNAbin':
as.phyDat(x, ...)
## S3 method for class 'phyDat':
as.character(x, ...)## S3 method for class 'phyDat':
as.DNAbin(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.

file

A file name.

format

File format of the sequence alignment (see details).

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.

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 patterns and can be usefull in simulation studies. write.phyDat calls the function write.dna or write.nexus.data and read.phyDat calls the function read.dna, read.aa or read.nexus.data see for more details over there. You may import data directly with read.dna or read.nexus.data and convert the data to class phyDat. The generic function 'c' can be used to to combine sequences and unique to get all unique sequences or haplotides.

See Also

DNAbin, as.DNAbin, read.dna, read.aa 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)