site.pattern: Site patterns
In bomeara/phybase: Basic functions for phylogenetic analysis

Description Usage Arguments Value Author(s) See Also Examples

The function returns site patterns.

1	site.pattern(seq)

seq

DNA sequences with rows representing taxa and columns representing sites

The function returns a matrix. Each row in the matrix represents a site pattern and the last number at each row is the frequency of the site pattern appeared in the DNA sequences.

Liang Liu lliu@uga.edu

mrca.2nodes, mrca.nodes

seq<- matrix("A",nrow=4,ncol=5)
seq[1,]<-c("A","A","G","C","C")
seq[2,]<-c("A","G","G","C","C")
seq[3,]<-c("T","A","G","C","C")
seq[4,]<-c("A","A","G","T","T")
site.pattern(seq)