ComPairWise-package     Compare phylogenetic or population genetic
                        DNA/RNA alignments
aln.to.matrix           Convert an alignment to a taxa-by-characters
                        matrix
check.format            Determine DNA/RNA alignment format
cpw                     Compare alternate alignments of phylogenetic or
                        population genetic data
deinterleave            Convert interleaved alignments to sequential
dots.to.bases           Convert alignment formats from dot-match to all
                        bases
endpoints               Find the breakpoints between identical and
                        different alignment columns
long.string             Make the +-o string
matrix.to.aln           Convert a data matrix to an alignment
nexus.sets              Create NEXUS sets block
read.nexus              Read a NEXUS-format character alignment
read.phylip             Read a PHYLIP-format character alignment
sample.aln              Sample DNA alignment
