site.pattern: Site patterns

In lliu1871/phybase: Basic functions for phylogenetic analysis

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 [e-mail]

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)

lliu1871/phybase documentation built on April 21, 2024, 3:16 a.m.