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UGENE is free open-source bioinformatics software. It works on a desktop computer with Windows, Mac OS X or Linux.

UGENE helps biologists to analyze various biological data, such as sequences, annotations, multiple alignments, phylogenetic trees, NGS assemblies, and others. The data can be stored both locally (on a personal computer) and on a shared storage (e.g. a lab database).

UGENE integrates dozens of well-known biological tools and algorithms, as well as original tools in context of genomics, evolutionary biology, virology and other branches of life science. UGENE provides a graphical interface for the pre-built tools so biologists without programming skills can access those tools more easily.

Using UGENE Workflow Designer, it is possible to streamline a multi-step analysis. The workflow consists of blocks such as data readers, blocks executing embedded tools/algorithms and data writers. Blocks can be created with command line tools or a script. A set of sample workflows is available in the Workflow Designer (for annotating sequences, conversion of data formats, NGS data analysis, etc.)

Besides the graphical interface, UGENE also provides a command-line interface. A workflow made by the Workflow Designer can be executed using the command-line interface.

In order to provide better performance, UGENE utilizes multicore CPUs and GPUs to optimize a few algorithms.