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After that you open the UGENE main window you can open select and analyze different files such as sequences, multiple sequence alignments, assembly 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 sequence as a file file with a nucleic or protein sequence you can see the following picture  where where there are the project view with your document, sequence view with your sequence and its annotations, options panel with many available options. Also you You can also use algorithms and instruments from the sequence context menu: 

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  <img src="/wiki/download/attachments/2523429/pic4_1.png"/>
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Example 1: For example, you want find orfs  in to find open reading frames (ORFs) in your sequence. For this do select the Analyze-->Find ORFsitem from the context menu:

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  <img src="/wiki/download/attachments/2523429/pic6.png"/>
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or by the toolbar Show ORFs icon:

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  <img src="/wiki/download/attachments/2523429/pic7.png"/>
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After that you can will see your sequence with ORFs:

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  <img src="/wiki/download/attachments/2523429/pic8_1.png"/>
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2. If you choose as 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:

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  <img src="/wiki/download/attachments/2523429/pic12.png"/>
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3. If you choose as an open click a file a short reads assembly, like BAM or SAM format you see the following picture:

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  <img src="/wiki/download/attachments/2523429/pic14 (3).png"/>
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These were the basic functions provided for you by UGENE. Read more about advanced options in the next chapter.