ComPairWise-package	ComPairWise-package
aln.files	aln.files
aln.to.matrix	aln.to.matrix
check.format	check.format
comp.all	comp.all
comp.mat	comp.mat
ComPairWise	ComPairWise-package
cpw	cpw
deinterleave	deinterleave
dots.to.bases	dots.to.bases
endpoints	endpoints
long.string	long.string
matrix.to.aln	matrix.to.aln
nexus.sets	nexus.sets
read.nexus	read.nexus
read.phylip	read.phylip
sample.aln	sample.aln
vectorize.alignment	vectorize.alignment
