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AltAVist - AltAVist : Alternative Alignment Visualization Tool

ClustalW - general purpose multiple sequence alignment program for DNA or proteins

dca - Divide-and-Conquer Multiple Sequence Alignment (DCA) is a program for producing fast, high quality simultaneous multiple sequence alignments of amino acid, RNA, or DNA sequences.

Dialign - DIALIGN is a multiple alignment program based on segment-to-segment comparison.

E2G - E2G - Efficiently Mapping large EST and cDNA sets to Genomic Sequences.

JAli - Jumping Alignments (JAli)is an alignment method for comparing a protein sequence to a protein family, represented by a multiple alignment. It can also be used for sensitive protein database searches. The algorithm is ] a generalization of the Smith-Watherman algorithm.

OMA - OMA is a library of C++-classes for the optimal alignment of sequences

PoSSuMsearch no description available

PoSSuMsearch2 - Significant speedup of database searches with HMMs by search space reduction with PSSM family models

SWIFT Suit - The SWIFT suit is a software collection for fast index-based sequence comparison.

TSDA - TSDA(target site duplication align) is an alignment tool to analyse recombinant DNA sequences.