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Clustal is a widely used multiple sequence alignment program. It is used for both nucleotide and protein sequences.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. It will also make use of multiple processors, where present. 

Clustal home page:

If you are using Windows OS, there are no additional configuration steps required, as ClustalO executable file is included to the UGENE distribution package. Otherwise:

Now you are able to use ClustaOl from UGENE.

Open a multiple sequence alignment file and select the Align with ClustalO item in the context menu or in the Actions main menu. The Align with ClustalO dialog will appear (see below), where you can adjust the following parameters:

Number of iterations — number of (combined guide tree/HMM) iterations.

Max number guidetree iterations — maximum guide tree iterations.

Max number of HMM iterations —maximum number of HMM iterations.

Number of CPUs being used - number of processors to use.

Set options automatically - set options automatically (might overwrite some of your options).



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