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Multiple sequence alignment (MSA Editor). The Alignment Editor is a powerful tool for visualization and editing DNA, RNA or protein multiple sequence alignments. To activate the Alignment Editor open any alignment file. For example you can use the $ugene/data/samples/CLUSTALW/COI.aln file provided with UGENE. After opening the file in UGENE the Alignment Editor window appears:

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The editor supports different multiple sequence alignment (MSA) formats, such as ClustalW, MSF and Stockholm. The editor provides interactive visual representation which includes:

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a. From the toolbar. Click to the tree icon:

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b. From the context menu:

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c. From the Options Panel:

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After calculation the tree appears in the MSA Editor in a separate window:

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