The latest UGENE 1.12 version is a major release that provides dozens of new features (major and minor), bug fixes and a set of usability and other improvements.

The major changes are:
* The new entity 'Datasets' in the Workflow Designer which replaces URL parameters
*The MSA editor has been upgraded with pairwise alignment algorithms and the sequence highlighting
*The Assembly Browser allows exporting consensus variations in VCF4 and Simple SNP formats
* Integration with BioMart: extensions for WEB-browsers (Mozilla Firefox and Google Chrome)

You can download the version here: http://ugene.unipro.ru/download.html