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Creating, editing, aligning of multiple sequence alignments

2. Multiple sequence alignment (MSA Editor).  If you open a multiple sequence alignment the following views are available: the project view with your documents, the MSA Editor with your alignment, options panel with additional info and algorithms. You can also use algorithms and instruments from the context menu or the toolbar:  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:

• 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. 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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