Belshaw R, Katzourakis A (2005) BlastAlign: a program that uses blast to align problematic nucleotide sequences. Bioinformatics 21:122-3

Authors: Aris Katzourakis & Robert Belshaw

Latest version: 1.4

Download program and documentation:

using legacy BLAST (blastalign.v1.4.tar)

using BLAST+ (blastalign+.tar)


BlastAlign uses NCBI Blast to align nucleotide sequences that have large indels or are otherwise difficult to align globally. The program selects the most representative sequence from the input sequences and then extracts the blast query anchored multiple alignment (in NEXUS and Phylip formats). Alternatively, the user can choose which sequence to use as an anchor. The program also outputs a matrix representing regions of homology along the sequences, which can be used to visually identify subgroups sharing particular large indels. An additional program, BlastAlignP uses tblastn to align nucleotide sequences to a single amino acid reference sequence, allowing an open reading frame to be maintained in the multiple alignment.

In addition, BlastAlign web-servers are available at the following sites:


BlastAlign was written for LINUX and will also run on Mac OSX and DOS. The program requires that Perl and Python are both installed (available on most UNIX based machines). It also requires the installation of NCBI blast (details for installation are in the readme file).