UGENE is a free software aimed to integrate most of the important
molecular biology tools within a single graphical environment that
runs fast both on Linux and Windows systems and is able to utilize
resources of modern multi-core hardware.
Some of new features in version 1.1:
* Graphical interface and integration of HMMER2 command line tools.
* Support for gzipped data files
The complete list of features is available here: http://ugene.unipro.ru/changelist.html