Alignment Editor Features

The Alignment Editor is a powerful tool for visualizing and editing DNA, RNA, or protein multiple sequence alignments. The editor supports various multiple sequence alignment (MSA) formats, such as ClustalW, MSF, and Stockholm. The full list of file formats supported in UGENE is here.

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;
  • Export of publication-ready images for alignments;
  • 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.
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