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See:
Description
Class Summary | |
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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 | |
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AlignmentException | Exception related to an alignment (currently only input errors) |
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.
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