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  • Aligning Sequences

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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.
  • 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.