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Multiple sequence alignment (MSA Editor).  If you open a multiple sequence alignment, for example  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, Alignment Editor appears. The following views are available: the project view with your documents, the Alignment Editor with your alignment, options panel with additional info and algorithmsaln file provided with UGENE. After opening the file in UGENE the Alignment Editor window appears:

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Alignment Editor - an object view used to visualize and edit DNA, RNA or protein multiple sequence alignments.

You can also use algorithms and instruments from the context menu or the toolbar: 

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Example 2:The editor supports different multiple sequence alignment (MSA) formats, such as ClustalW, MSF and Stockholm. The editor provides interactive visual representation which includes:

• Navigation through an alignment;
• Optional coloring schemes (for example Clustal, Jalview like, etc.);
• Flexible zooming for large alignments;
• Export publication-ready images of alignment;
• Several consensus calculation algorithms.

Using the Alignment Editor you can:

• Perform multiple sequence alignment using integrated MUSCLE and KAlign algorithms;
• Edit an alignment: delete/copy/paste symbols, sequences and subalignments;
• Build phylogenetic trees;
• Generate grid profiles;
• Build Hidden Markov Model profiles to use with HMM2/HMM3 tools.

Example 2: Build a tree from your alignment. You can do this by three different ways:

a. From the toolbar:

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