EMBOSS is "The European Molecular Biology Open Software Suite".

EMBOSS is a free Open Source software analysis package specially
developed for the needs of the molecular biology (e.g. EMBnet) user
community. The software automatically copes with data in a variety of
formats and even allows transparent retrieval of sequence data from
the web. Also, as extensive libraries are provided with the package,
it is a platform to allow other scientists to develop and release
software in true open source spirit. EMBOSS also integrates a range of
currently available packages and tools for sequence analysis into a
seamless whole. EMBOSS breaks the historical trend towards commercial
software packages.

Within EMBOSS you will find around hundreds of programs (applications)
covering areas such as:

- Sequence alignment
- Rapid database searching with sequence patterns
- Protein motif identification, including domain analysis
- Nucleotide sequence pattern analysis -- for example to identify CpG
  islands or repeats
- Codon usage analysis for small genomes
- Rapid identification of sequence patterns in large scale sequence
  sets
- Presentation tools for publication

Optional, run-time dependencies are clustalw and primer3 -- needed if
you want to use the wrappers emma and eprimer32.

For details and citation:
EMBOSS: The European Molecular Biology Open Software Suite (2000)
Rice,P. Longden,I. and Bleasby,A. Trends in Genetics 16, (6) pp276-277