An alignment containing multiple SymbolLists.

AlignmentElement is a class which represents a SymbolList and its location within an Alignment This is for use in UnequalLengthAlignments and ARAlignments.

ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.

EditableAlignment is an interface that defines methods for shifting bases within an Alignment.

UnequalLengthAlignment has the following behavior.

Iterator implementation looping over symbol lists in an alignment using the labels.

This Interface provides methods for the alignment of bio-sequences.

This class stores the result of an alignment procedure that creates a pairwise alignment of two sequences.

FlexibleAlignment is a class which implements UnequalLengthAlignment, ARAlignment and EditableAlignment It places no restriction on where any sequence can be in the alignment so there could be gaps in the alignment.

Needleman and Wunsch defined the problem of global sequence alignments, from the first till the last symbol of a sequence.

A simple implementation of an Alignment.

SimpleSimpleAlignment is a simple implementation of AlignmentElement.

Smith and Waterman developed an efficient dynamic programming algorithm to perform local sequence alignments, which returns the most conserved region of two sequences (longest common substring with modifications).

This object is able to read a substitution matrix file and constructs a short matrix in memory.

The usual reason for throwing an IllegalAlignmentEditException is that you are trying to shift a group of bases in such a way that it would require deleting bases.