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| 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 |
| ComPairWise | Compare phylogenetic or population genetic DNA/RNA alignments |
| 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 |