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Tools  › BALIGN


Many bioinformatics applications require computation of pairwise alignment score matrices for large sets of sequences. Existing pairwise alignment tools either generate irrelevant data besides the alignment scores or are not designed for batch processing. BALIGN is a pairwise sequence alignment tool optimized for computation of large alignment score matrices. It works on any type of sequence whose substitution matrix is given. In addition to the standard global and local alignments with affine gap penalty, it also supports alignment of compound sequences that consist of two parallel sequences, such as the compound sequence consisting of an amino acid sequence and the corresponding secondary structure.


BALIGN is licensed under the GNU Public License.


Latest Version (1.0.0)