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.

Utilities

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.

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

Versions

Version	module name
2.4.0	exonerate/2.4.0

Links

https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate

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