Exonerate is a tool for various types of pairwise sequence comparison.
It allows us to align sequences using many alignment models including
est2genome, protein2genome, and so on.

Citation:

Slater, G. S. C. and Birney, E. (2005) Automated generation of heuristics
for biological sequence comparison. BMC Bioinformatics 6:31.

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