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A set of project/file level operations.

Example: create, open, etc. a project; open a document; access remote database to download a file.


Various actions associated with the active window.

Example: export, remove, edit, analyze a sequence using different plugins (for the Sequence View); edit, align, change the consensus mode (for the Alignment Editor).

SettingsApplication, plugins and tools settings.

Various tools, independent of an active window. This menu is extended by different plugins.

Example: HMMER2 / HMMER3 tools, SITECON, Workflow Designer.


A list of active windows and basic manipulations with the windows.

Example: close all windows, tile windows, select next window.

HelpApplication help and check for updates.


You can use UGENE sample files. There are the following sample data: ABIF, ACE, Assembly, CLUSTALW, EMBL, FASTA, FASTQ, Genbank, GFF, HMM, MMDB, MSF, Newick, PDB, Raw, SCF, Stockholm, Swiss-Prot. These data files are located in the main UGENE directory: ugene/data/samples.