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

  • Port of the popular MUSCLE3 algorithm.
  • KAlign plugin: effective work with huge alignments.
  • ClustalW and MAFFT: these algorithms appeared in the version 1.7.2 of UGENE with the External Tools plugin.
  • T-Coffee: this alignment algorithm is available since version 1.8.1 of UGENE with the External Tools plugin.

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

Also you may find useful the following video tutorials devoted to the multiple sequence alignment:

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