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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.

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

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1. <B>Nucleotide or protein sequence</B> If you choose a file with a nucleic or protein sequence you can see the following picture where there are with 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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or by the toolbar Show ORFs icon:

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

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