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ClustalW on the cluster

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A parallel implementation of ClustalW 1.82 is installed on the cluster. This implementation runs incredibly fast! See this web page for the reference.

1. Create your input data file. Make sure this file has UNIX line breaks (use TextWrangler). Seven formats are automatically recognized: NBRF-PIR, EMBL-SWISSPROT, Pearson (Fasta), Clustal (*.aln), GCG-MSF (Pileup), GCG9-RSF and GDE flat file.
2. 
   
3. Upload (sftp - use Fugu) your file to the cluster, ideally to an empty directory.
4. 
   
5. To run your job, move into the directory with the input data file and type "runjobs.clustalw name_of_file", where "name_of_file" is the name of your input data file. By default ClustalW will save your alignment in ClustalW format. If you would like to choose another output format, type the name of the format you want after "name_of_file". The output file options are "gcg", "gde", "nexus", "pir" (NBRF), and "phylip".
6. 
   
7. When the run finishes, an email will be sent to your UMSL email account (i.e., yourgatewayid@umsl.edu). Depending on the size of your data set it may take some time to run.

Your job will use a total of six processors.