View, Edit and Align Multiple Sequence Alignments

Multiple Sequence Alignment (MSA Editor). The Alignment Editor is a powerful tool for visualizing 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:

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

  • Navigation through an alignment;
  • Optional coloring schemes (for example, Clustal, Jalview-like, etc.);
  • Flexible zooming for large alignments;
  • Exporting publication-ready images of alignment;
  • Multiple 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 sub-alignments;
  • 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 in three different ways:

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

b. From the context menu:

c. From the Options Panel:

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

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