Entry: ComPairWise-package
Aliases: ComPairWise-package ComPairWise
Keywords: package
Description: Compare phylogenetic or population genetic DNA/RNA alignments
URL: ../../../library/ComPairWise/html/ComPairWise-package.html

Entry: aln.files
Aliases: aln.files
Keywords: internal
Description: Prompt user for filenames if necessary, and combine all names into a vector.
URL: ../../../library/ComPairWise/html/aln.files.html

Entry: aln.to.matrix
Aliases: aln.to.matrix
Keywords: manip
Description: Convert an alignment to a taxa-by-characters matrix
URL: ../../../library/ComPairWise/html/aln.to.matrix.html

Entry: check.format
Aliases: check.format
Keywords: file
Description: Determine DNA/RNA alignment format
URL: ../../../library/ComPairWise/html/check.format.html

Entry: comp.all
Aliases: comp.all
Keywords: internal
Description: Groupwise comparison of alignment matrices
URL: ../../../library/ComPairWise/html/comp.all.html

Entry: comp.mat
Aliases: comp.mat
Keywords: internal
Description: Pairwise comparison of alignment matrices
URL: ../../../library/ComPairWise/html/comp.mat.html

Entry: cpw
Aliases: cpw
Keywords: misc
Description: Compare alternate alignments of phylogenetic or population genetic data
URL: ../../../library/ComPairWise/html/cpw.html

Entry: deinterleave
Aliases: deinterleave
Keywords: manip
Description: Convert interleaved alignments to sequential
URL: ../../../library/ComPairWise/html/deinterleave.html

Entry: dots.to.bases
Aliases: dots.to.bases
Keywords: manip
Description: Convert alignment formats from dot-match to all bases
URL: ../../../library/ComPairWise/html/dots.to.bases.html

Entry: endpoints
Aliases: endpoints
Keywords: dplot
Description: Find the breakpoints between identical and different alignment columns
URL: ../../../library/ComPairWise/html/endpoints.html

Entry: long.string
Aliases: long.string
Keywords: manip
Description: Make the +-o string
URL: ../../../library/ComPairWise/html/long.string.html

Entry: matrix.to.aln
Aliases: matrix.to.aln
Keywords: manip
Description: Convert a data matrix to an alignment
URL: ../../../library/ComPairWise/html/matrix.to.aln.html

Entry: nexus.sets
Aliases: nexus.sets
Keywords: utilities
Description: Create NEXUS sets block
URL: ../../../library/ComPairWise/html/nexus.sets.html

Entry: read.nexus
Aliases: read.nexus
Keywords: file
Description: Read a NEXUS-format character alignment
URL: ../../../library/ComPairWise/html/read.nexus.html

Entry: read.phylip
Aliases: read.phylip
Keywords: file
Description: Read a PHYLIP-format character alignment
URL: ../../../library/ComPairWise/html/read.phylip.html

Entry: sample.aln
Aliases: sample.aln
Keywords: datasets
Description: Sample DNA alignment
URL: ../../../library/ComPairWise/html/sample.aln.html

Entry: vectorize.alignment
Aliases: vectorize.alignment
Keywords: internal
Description: Turn DNA/RNA alignment into numbers
URL: ../../../library/ComPairWise/html/vectorize.alignment.html
