Utopia is a collection of interactive tools for analysing protein sequence and structure. Up front are user-friendly and responsive visualisation applications, behind the scenes a sophisticated model that allows these to work together and hide much of the tedious work of dealing with file formats and web services.

Chipster allows you to perform DNA microarray data analysis with R/Bioconductor and other tools through an intuitive graphical user interface.

This character-based menu program is distributed as an EMBASSY add-on to the EMBOSS package. Its only potential use is for terminals without graphical capability

http://wiki.moltalk.org/index.php?page=EMBOSS

MolTalk: a computational environment for Structural Bioinformatics. It uses EMBOSS for handling sequences and alignments.