PairWise PairWise is an interactive program that performs various sorts of pairwise alignments using biological sequences. It can align a protein profile to either a protein sequence or to the 3-frame translation of a DNA sequence, allowing shifts between the frames. SearchWise SearchWise uses the local batch system to run sequence database searches with either protein, protein alignment or DNA query versus protein or DNA databases. You can get the source code for most operating systems here . It can also plot tree showing the clustering relationships used to create alignment.
LineUp is a screen editor for editing multiple sequence alignments.
You can edit up to 30 sequences simultaneously. New sequences can be typed in by hand or added from existing sequence files. Gap uses the algorithm of Needleman and Wunsch to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. A multiple sequence alignment editor. You can get the source code at biom3.univ-lyon1.fr .