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When you open UGENE for the first time, there is an empty UGENE window with the main menu bar . Using these menus you can run many algorithms, configure different settings and get help.on the top of the window: 

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Now Using these menus you can select and analyze different files such as sequences, multiple sequence alignments, short reads assemblies and etc. To open a file click to the File-->Open or click to the Open icon and choose the file:

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1. If you choose a file with a nucleic or protein sequence you can see the following picture where there are the project view with your document, sequence view with your sequence and its annotations, options panel with many available options. You can also use algorithms and instruments from the context menu: 

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Example 1: For example, you want to find open reading frames (ORFs) in your sequence. For this select the Analyze-->Find ORFs item from the context menu:

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or by the toolbar Show ORFs icon:

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After that you will see your sequence with ORFs:

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2. If you open a file with a multiple sequence alignment you can see the following picture where there are Options Panel, Toolbar and context menu with many instruments and algorithms:

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Example 2: For example, you may want to build a tree from your alignment. You can do this by three different ways:

a. From the toolbar:

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b. From the context menurun many algorithms, configure different settings and get help: 

MenuDescription
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).

SettingsApplication, 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.

HelpApplication help and check for updates.

The menus can be dynamically populated with new actions added by plugins. 

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:

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c. From the Options Panel:

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When you choose the building tree parameters in the dialogs the tree appears:

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3. If you click a file a short reads assembly, like BAM or SAM format you see the following picture:

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Example 3: For example, you want to highlight the strand direction reads. You can do this by two ways: by the context menu or by the Options Panel menu.

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These were the basic functions provided for you by UGENE. Read more about advanced options in the next chapter.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 files are located in the main UGENE directory: ugene/data/samples.

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