A non-metric sequence alignment program - Davison, D.; Thompson, K.H. (Elsevier)
An algorithm for nucleic acid and protein sequence alignment is presented. It is a nonmetric local similarity minimal-difference algorithm and in the current implementation, assembles the matching regions found into a pseudo-global format. Its strengths are its speed of execution and the especially convenient presentation of its output. The algorithm is intended for use in sequence melding and local (small-region) similarity searching. It is not designed to replace a metric Needleman-Wunsch-Sellers-type similarity algorithm. The program is written in FORTRAN and is designed to be easily transportable to a variety of computer systems.
http://dx.doi.org/10.1016/S0092-8240(84)80061-0
Keywords: W; SA-SP