New version includes several critical bug fixes and some new features:

• UGENE Genome Aligner is optimized towards better performance. Now it can use - modern GPUs to boost the computations
• Workflow Designer imporovements:
  
  • Added new workflow elements: merge and write annotations
  • Added support of FASTA files as queries for Smith-Waterman search
• Query Designer improvements:
  
  • Added HMM query element
  • Search query can be customized for specific strand
• Automatic annotation highlighting for Restriction Enzymes plugin is introduced. Once configured, restriction sites search is performed for newly opened sequences automatically --- no need to launch search every time for new molecule.
• A lot of bug fixed and minor improvements implemented!

Check this page to download the latest version of Unipro UGENE : http://ugene.unipro.ru