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 or in the context menu.
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