Package Alignments

Provides class for dealing with "alignments" and the sites in an alignment.

See:
          Description

Class Summary
Alignment Represents an "alignment", used very losely.
Ambiguous Stores details of ambiguous characters
DuplicationAlignment Represents a duplication "alignment" - a set of gene families with their associated size in each species
FastaAlignment Represents a sequence alignment in FASTA format
PhylipAlignment Represents a sequence alignment in Phylip format
SequenceAlignment Deprecated. Replaced by PhylipAlignment to allow for easier use of multiple formats.
Site Represents a "site" in an "alignment".
 

Exception Summary
AlignmentException Exception related to an alignment (currently only input errors)
 

Package Alignments Description

Provides class for dealing with "alignments" and the sites in an alignment. These include sequence data and gene family size data. Also includes a class used to deal with ambiguous data in an alignment.