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Unipro UGENE Online User Manual


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User manual sections overview

Basic Functions

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

Sequence View

Description of the view used to visualize and edit DNA, RNA or protein sequences along with their annotations.

Sequence View Extensions

Description of the extensions of the sequence view like chromatograms, 3D models, statistical data, etc.

Alignment Editor

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

Assembly Browser

Description of the browser used to visualize and efficiently browse large next generation sequence assemblies.

Phylogenetic Tree Viewer

Description of the view intended to display a phylogenetic tree.

Distributed Computing

Description of the running different tasks on remote machine.


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

UGENE Command Line Interface

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.).