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This section provides introduction to UGENE. It contains the program terminology, overview of the main menu items and description of the application settings dialog.

Description of the view used to visualize and edit DNA, RNA or protein sequences along with their properties like annotations, chromatograms, 3D models, statistical data, etc.

Description of the view used to visualize and edit DNA, RNA or protein multiple sequence alignments.

Description of the view intended to display a phylogenetic tree.

UGENE provides a number of plugins, i.e. dynamically loaded modules that add new functionality.

UGENE contains a powerful command line tool. Most tasks can be performed using the command line interface.

Appendix A. Supported file formats

This appendix contains the list of file formats supported by UGENE (specific formats for sequences, multiple sequence alignments, etc.; native UGENE file formats; etc.).