BlastAlign

BlastAlign is a program for the global alignment of sequences that contain large indels or are otherwise difficult to align. It uses NCBI blastn to build a matrix representing regions of homology along the sequences, from which it selects the most representative sequence and extracts the query-anchored multiple alignment for this sequence. The matrix is printed so that subgroups can be identified visually and other sequences can be designated as the most representative if desired. The program is compatible with UNIX (including Mac OSX) and DOS, and consists of elements from both Perl and Python. Another Perl program, BlastAlignP, uses tblastn to align nucleotide sequences to a single amino acid sequence, thus preserving the open reading frame in the multiple alignment.