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.
- 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 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: