exonerate

Exonerate allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. Much of the functionality of the Wise dynamic programming suite was reimplemented in C for better efficiency. Exonerate is an intrinsic component of the building of the Ensembl genome databases, providing similarity scores between RNA and DNA sequences and thus determining splice variants and coding sequences in general. An In-silico PCR Experiment Simulation System (see the ipcress man page) is packaged with exonerate. This package also comes with a selection of utilities for performing simple manipulations quickly on fasta files beyond 2Gb