emboss

The European Molecular Biology Open Software Suite (EMBOSS) is a high quality, well documented package of open source software tools for molecular biology. It includes over 200 applications for molecular sequence analysis and other common tasks in bioinformatics. It integrates the core applications with a range of popular third party software packages under a consistent and powerful command line interface. The software has many useful features; for example, it automatically copes with data in a variety of formats and allows for transparent retrieval of sequence data from the web. (Summary from the program web page.)

The official web page: http://emboss.open-bio.org/