When you open UGENE for the first time, there is an empty UGENE window with the main settingsmenu bar. Using these settings menus you can run the many algorithms, configure different settings and use the help menu if you need itget help.
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Now 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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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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These were the basic functions provided for you by UGENE. Read more about advanced options in the next chapter.