UGENE 1.7.0 - Changelog

What's new in UGENE 1.7.0:

June 1st, 2010

The new release includes the long awaited DNA assembly functionality. Since now short read alignment can be performed with UGENE. Two methods are available:

· Genome aligner plugin, based on unique algorithm;
· Port of popular open-source tool Bowtie.

· A lot of improvements were made to console version of UGENE. It has become much more flexible and powerful. Since now it is possible to use command line version of UGENE in complex scripts and shell scenarios. There are useful prebuilt scenarios available: align, convert, find repeats etc. Check documenation for more details.

Other cool features available:

· New advanced sequence analysis algorithm based on weight matrices;
· Circular view improvements: zoooming, rotating and more;
· Support for advanced search options of NCBI BLAST in redesigned Remote Request plugin.
· Alignment logo feature;
· New fancy widget: global sequence overview;
· Tree viewer is re-worked: stand-alone interface, new visualization modes.
· GFF format now supports writing;
· Scripting framework is introduced;
· and a lot more...

What's new in UGENE 1.6.2:

March 30th, 2010

· This release brings several really long-awaited features such as circular view and
· sequence reverse translation.

· Note for our linux users: UGENE is now available as a universal binary package
· intended to be installed independently of package managers.

New features:
· New plugin: sequence circular view;
· Workflow designer: support for launching tasks remotely;
· MSA Editor: consensus mode added, usability improvements;
· Phylogenetic tree viewer: zooming, normalization, export to SVG;
· Export plugin: reverse protein translation;
· Support for import annotation tables from CSV files;
· Enzymes plugin: support for creation of custom enzyme databases in BAIROCH format;
· And many others!

What's new in UGENE 1.6.0:

January 23rd, 2010

New plugins:
· Phylip plugin for building phylogenetic trees. Based on original Phylip 3.6 package .
· Neighbor Joining algorithm;
· Phylogenetic trees visualization;
· Integration with Multiple Alignment Editor.

· Distributed computing in UGENE
· Support for launching HMMER 3 , Smith-Waterman , MUSCLE tasks on remote machines.
· Remote tasks support;

New features and bug fixes:
· Search for tandem repeats introduced in Repeat Finder plugin;
· Project files transferability support;
· "Export project" feature;
· Interaction with remote databases: NCBI, PDB, Swiss Prot;
· BioStruct3D plugin: anaglyph stereo mode;
· and a lot more...

What's new in UGENE 1.5.2:

November 6th, 2009

New plugins:

· MUSCLE 4 - a port of the newest tool for multiple sequence alignment by Robert C. Edgar;
· CUDA Support - an utility plugin which makes possible using NVIDIA graphical processing units for accelerating computational algorithms.

New features and bug fixes:

· CUDA-accelerated Smith-Waterman algorithm is ready to use for Windows users;
· The one of the most awaited features: sequence editing has been added;
· Exporting annotation tables to CSV has been provided;
· HMM2 models support has been added to HMM3;
· And many others. See the changelog for a full list of improvements.