Note: Clustal Omega replaces ClustalW in Geneious Prime 2020 onwards
Clustal Omega is a general purpose multiple sequence alignment (MSA) program for protein and DNA/RNA. It produces high quality MSAs and uses multiple execution threads, so is capable of handling datasets of hundreds of thousands of sequences in reasonable time. Clustal Omega can be run from within Geneious Prime without having to export your sequences and can also be used with translation alignment (see section 9.2.6 ).
To perform an alignment using Clustal Omega, select the sequences or alignment you wish to align, then select Align/Assemble → Multiple Align.... Select Clustal Omega as the alignment type, and the options available for a Clustal Omega alignment will be displayed.
To have Clustal Omega automatically select the speed and accuracy settings based on the size of your dataset, open the More Options tab and select Automatically adjust settings based on number of sequences.
For further information on the Clustal Omega settings and additional command line options, see the Clustal Omega documentation. The command line input and output for your alignment can be viewed in the Info tab on the alignment result document in Geneious.