bootstrap.mulgene: Bootstrap sequences from multiple loci
In bomeara/phybase: Basic functions for phylogenetic analysis

Description Usage Arguments Details Value Author(s) See Also Examples

The function bootstraps sequence columns for each locus sampled from the original multilocus data. It consists of two step. First, it bootstraps loci. Then it bootstraps sequences for each locus.

1	bootstrap.mulgene(sequence,gene,name,boot,outfile="")

`sequence`	data matrix
`gene`	location of each locus
`name`	taxa names of sequences
`boot`	the number of bootstrap samples
`outfile`	output file

In the sequences matrix, the rows are "Taxa" and the columns are "sites".

The function generates a data file in phylip format.

Liang Liu lliu@uga.edu

bootstrap

#construct the DNA sequences of three taxa
seq <- matrix("A",ncol=4,nrow=3)
rownames(seq)<-c("taxa1","taxa2","taxa3")
seq[,2]<-"G"
seq[,3]<-"C"
seq[,4]<-"T" 

name<-rownames(seq) #taxa names of the sequences

#construct two loci. The first two nucleotides represent the first locus, 
#while nucleotide 3 and 4 represent the second locus.
gene<-matrix(0,ncol=2,nrow=2)
gene[1,]<-c(1,2)
gene[2,]<-c(3,4)
gene          
bootstrap.mulgene(seq,gene,name,boot=2,outfile="bootdata.txt")