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- 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 Actions main menu, in the context menu or by Align main toolbar button .
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