Needleman and Wunsch definied the problem of global sequence alignments, from the first till the last symbol of a sequence. This class is able to perform such global sequence comparisons efficiently by dynamic programing. If inserts and deletes are equally expensive and as expensive as the extension of a gap, the alignment method of this class does not use affine gap panelties Otherwise it does. Those costs need four times as much memory, which has significant effects on the run time, if the computer needs to swap.

Original BioJava version by Andreas Dräger, Gero Greiner and Mark Schreiber. Port to C# by Doug Swisher.