BlastAlign: a program that uses blast to align nucleotide sequences that have large indels (INsertions/DELetions) or are otherwise difficult to align.
The citation for BlastAlign is as follows:
Belshaw R, Katzourakis A. (2005). BlastAlign: a program that uses blast to align problematic nucleotide sequences. Bioinformatics. 21:122-123.
Go to the BlastAlign web interface page.