Shared storage: sharing of bioinformatics data in a lab. For details, see this page.
Overview for a multiple alignment was added, a lot of configuration options are available.
A multiple alignment consensus can now be exported.
PhyML Maximum Likelihood was integrated.
It is now possible to re-root a tree.
Circular View and circular sequences: a possibility to mark a nucleotide sequence as circular was added. This mark affects how a pattern is searched in the sequence – results located over the end-start junction of it are also found.
Plasmid features: auto-annotation of the plasmid features like promoters, regulatory regions, primers, etc.
Export images: exporting of images was improved (multiple alignments, circular molecules, etc.)
BWA-MEM tool for aligning short reads was integrated. The tool is available in the GUI dialog and in the Workflow Designer.
Different workflow elements for sorting, merging and filtering and trimming of NGS data were added (BAM and FASTQ files).
UGENE Public Storage: the storage can be remotely accessed from any UGENE instance. It contains common genomes and hundreds of plasmids.