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.
See the Exonerate User Guide for examples and tips for how to make the most of this software.
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
Exonerate is written in C, and currently uses the glib library for portablility. It is portable to all UNIX-like systems, and has been used on various Linux distributions, TRU64, OSX, and BSD.
It is licensed under the GPL.
You can download the source code or a precompiled version.
Exonerate version 2.2 includes fixes for problems with excessive memory consumption when compiled against glib-2, and fixes a bug with using exonerate-server with unmasked sequences.
Arch Linux PKGBUILD file
Other platforms and related software
iPCRess, an In-silico PCR Experiment Simulation System, is packaged with Exonerate (see the IPCR manual).
The Exonerate package comes with a selection of utilities for performing simple manipulations quickly on fasta files beyond 2Gb. Hopefully their function is easy to guess from the name, but you can find more information on their usage can by running them with the --help option.
Questions about the exonerate package should be directed to Ensembl Helpdesk.
Thanks to Mick Elliot for the Arch Linux PKGBUILD file, and to Jeffrey R. de Wet for the windows/cygwin build. Thanks also to Luc Grenier for the gentoo ebuild file.