site.pattern {phybase} | R Documentation |
The function returns site patterns.
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@oeb.harvard.edu
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)