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a generic tool for sequence alignment

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About

• exonerate is a generic tool for pairwise sequence comparison.
• It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.
• If you have questions, you can email guy@ebi.ac.uk

Documentation

• See the beginner's, advanced, and NEW:server user guides.
• For further details about using exonerate and examples, see man pages for exonerate, and exonerate-server.
• This paper BMC Bioinformatics 2005, 6:31. describes many of the algorithms in exonerate.

Download

• 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. (Please refer to the original site for details).
• Please email me if you would like to receive announcement emails when new versions of exonerate are released.
• Thanks to Luc Grenier for the gentoo ebuild file.

Miscellaneous

• iPCRess : an In-silico PCR Experiment Simulation System
  (see the ipcress man page) is packaged with exonerate.
• The exonerate package also 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 more information on their usage can be found by running them with the --help option. They are:

      esd2esi       fasta2esd        fastaannotatecdna fastachecksum fastaclean
      fastaclip     fastacomposition fastadiff         fastaexplode  fastafetch
      fastahardmask fastaindex       fastalength       fastanrdb     fastaoverlap
      fastareformat fastaremove      fastarevcomp      fastasoftmask fastasort
      fastasplit    fastasubseq      fastatranslate    fastavalidcds