phyDat {phangorn} | R Documentation |
These functions transform several DNA formats into the phyDat
format.
allSitePattern
generates an alignment of all possible site patterns.
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)
data |
An object containing sequences. |
x |
An object containing sequences. |
type |
Type of sequences ("DNA", "AA" or "USER"). |
levels |
Level attributes. |
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. |
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 useful 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 haplotypes.
The functions return an object of class phyDat
.
Klaus Schliep klaus.schliep@gmail.com
DNAbin
, as.DNAbin
, read.dna
, read.aa
and read.nexus.data
and
the example of pmlMix
for the use of allSitePattern
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)