Aligning Sequences

The Alignment Editor integrates several popular multiple sequence alignment algorithms. Below is a list of available algorithms and links to their documentation:

  • Port of the popular MUSCLE3 algorithm.
  • KAlign plugin: effective for working with large alignments.
  • ClustalW and MAFFT: These algorithms appeared in version 1.7.2 of UGENE with the External Tools plugin.
  • T-Coffee: This alignment algorithm has been available since version 1.8.1 of UGENE with the External Tools plugin.
  • ClustalO: Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours.

To align sequences, choose a preferred alignment method in the Actions main menu, in the context menu, or by using the Align main toolbar button.

You may also find the following video tutorials on multiple sequence alignment useful:

« Saving Alignment Adding Sequence(s) to Alignment »