EMBOSS -- European Molecular Biology Open Software Suite -- is a free open source software analysis package specially developed for the needs of the molecular biology and bioinformatics community .
Running EMBOSS programs
The Bio::Factory::EMBOSS module is a generic interface to EMBOSS applications for local running of the tools. Remote interfaces to EMBOSS are available through the PISE interface and the Bio::Tools::Run::AnalysisFactory::Pise module.
This tool provides spliced EST to Genome alignments so that alignments account for splice-sites when constructing an alignment and has an explict model for gap insertions at likely splice-sites. Is part of EMBOSS, but see the EST2genome page for more information.
Perl and EMBOSS (outside of BioPerl)
XS-based Perl modules that interacts with the EMBOSS packages exist which are not directly related to BioPerl (Bio::Emboss). Not much is known about them, but they appear to be regularly maintained.