dialign

Name dialign
Description Segment-based multiple sequence alignment DIALIGN2 is a command line tool to perform multiple alignment of protein or DNA sequences. It constructs alignments from gapfree pairs of simi Note: The -stdo option must be used to send the output to stdout so that it can be redirected to your desired location.
Homepage http://bibiserv.techfak.uni-bielefeld.de/dialign/  
Remote Documentation