BIONUMERICS offers probably the finest and most comprehensive multiple sequence alignment tool that currently exist for PCs. It combines clustering of thousands of nucleotide or protein sequences of almost unlimited length with multiple alignment and display of homology matrices.
Versatile user interface & direct editing
The versatile user interface allows sequences in multiple alignments to be displayed as raw chromatogram files as well as translated protein sequences. Direct editing is possible in any visualization. Multiple alignments associated with dendrograms can be edited manually in drag-and-drop mode, and a multistep undo/redo function makes editing even more convenient.
In addition to well-established alignment algorithms such as the Wilbur Lipman and Needleman Wunsch algorithm, the software contains extremely fast and reliable proprietary algorithms.