Exonerate: a generic tool for sequence alignment

Exonerate is a generic tool for pairwise sequence comparison. It allows
you to align sequences using a many alignment models, either exhaustive
dynamic programming or a variety of heuristics.

The Exonerate package comes with a selection of utilities for performing
simple manipulations quickly on fasta files beyond 2Gb.

Many of the algorithms in exonerate are described in:
Slater GS and Birney E (2005) Automated generation of heuristics for
biological sequence comparison. BMC Bioinformatics 6:31;
doi: 10.1186/1471-2105-6-31