Clustal Omega or ClustalO (see method has been developed to overcome the bottleneck that occurs in some pipelines when presented with data sets consisting of many thousands of sequences. The strength of ClustalO is that it can align virtually any number of sequences at high speed and with accurate alignments as a result [Sievers et al., 2011].

The ClustalO program in the Additional Alignments plugin has no user defined settings. Hence, to run the ClustalO program, you simply have to select the sequences to align and decide whether to Open or Save the result. Please note that the result consists of two output files: an alignment file and a phylogenetic tree file.