Unipro's Ugene is a free bioinformatics modeling and visualization tool. You can use it to visualize, analyze, and annotate DNA and protein sequences. It's widely compatible with a variety of platforms, tools, and methods and includes an integrated Muscle alignment tool, integrated Hmmer2 package, an OpenGL viewer for PDB macromolecular structures, and a custom workflow designer.
Ugene isn't difficult to set up, though much of what it does depends on access to other files and tools. Ugene's functions are based around Projects, Tasks, and Logs. Under Application Settings, we could configure everything from system resource allocation to OpenGL and CUDA settings (for Nvidia graphics cards only). The External Tools menu let us set up how Ugene interacts with the genetic information tools it's compatible with, such as Blast, Bowtie, ClusatlW, MrBayes, and T-Coffee. There's also a remote machine monitor option.
We quickly found ourselves in over our heads with Ugene, though not because the program is difficult to use in any way but because we lacked two critical things: detailed knowledge of genetics and access to existing sequences, models, and data. Most of the tools we tried require data to create visualizations, and obviously the program's analysis features require something to analyze. But Ugene also offers considerable documentation and assistance, both local and online, beginning with the PDF-based user manual. Ugene also includes a Workflow Designer Manual and Query Designer Manual. Its Web site offers a community forum, online support, and free and commercial support services, so there's something for everyone from impoverished students to top labs. We were impressed with Ugene's capabilities to give scientists and students a flexible, free genetic modeling solution on the cutting edge of biology. Most of the users who can make good use of Ugene will be able to see at a glance what it can do for their studies or research.