site.pattern {phybase}R Documentation

Site patterns

Description

The function returns site patterns.

Usage

site.pattern(seq)

Arguments

seq DNA sequences with rows representing taxa and columns representing sites

Value

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.

Author(s)

Liang Liu lliu@oeb.harvard.edu

See Also

mrca.2nodes, mrca.nodes

Examples

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)

[Package phybase version 1.1 Index]