An illustration of relationships between alignment methods. The applications / corresponding computational restrictions shown are (green) short pairwise alignment / detailed edit model; (yellow) database search / divergent homology detection; (red) whole genome alignment / alignment of long sequences with structural rearrangements; and (blue) short read mapping / rapid alignment of massive numbers of short sequences. Although solely illustrative, methods with more similar data structures or algorithmic approaches are on closer branches. The BLASR method combines data structures from short read alignment with optimization methods from whole genome alignment.
Chaisson and Tesler BMC Bioinformatics 2012 13:238 doi:10.1186/1471-2105-13-238