When open UGENE for the first time, there is an empty UGENE window with the main menu bar on the top of the window:
| HTML |
|---|
margin-top: 360mm;<center> <center><br> <img src="/wiki/download/attachments/2523429/ugene_main_window.gif"/> <br> </center> |
Using these menus you can run many algorithms, configure different settings and get help:
| Menu | Description |
|---|---|
| File | A set of project/file level operations. Example: create, open, etc. a project; open a document; access remote database to download a file. |
| Actions | 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). |
| Settings | Application, plugins and tools settings. |
| Tools | Various tools, independent of an active window. This menu is extended by different plugins. Example: HMMER2 / HMMER3 tools, SITECON, Workflow Designer. |
| Window | A list of active windows and basic manipulations with the windows. Example: close all windows, tile windows, select next window. |
| Help | Application help and check for updates. |
...
You can select and analyze different files such as sequences, multiple sequence alignments, short reads assemblies and etc. To open a file click on the File-->Open or click on the Open icon and choose the file:
| HTML |
|---|
<center> <br> <img src="/wiki/download/attachments/2523429/open_file.gif"/> <br> </center> |
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.
...