Package Alignments

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

See: Description

Class Summary

Class	Description
Alignment	Represents an "alignment", used very loosely.
Ambiguous	Stores details of ambiguous characters
DuplicationAlignment	Static classes for reading/writing duplication "alignments" - a set of gene families with their associated size in each species
FastaAlignment	Static classes for reading/writing sequence alignment in FASTA format
GenericAlignment	Static classes for reading/writing sequence alignment in a generic format.
PhylipAlignment	Static classes for reading/writing sequence alignment in Phylip format
Site	Represents a "site" in an "alignment".
UniqueSite	Used to represent a unique site in an alignment.

Exception Summary

Exception	Description
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.