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ClustalW FAQ (Frequently Asked Questions)

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What are the default parameters used by ClustalW?

When "def" values are used, we let ClustalW (1.82) use its own default values:
  • DNA Gap Open Penalty = 15.0
  • DNA Gap Extension Penalty = 6.66
  • DNA Matrix = Identity
  • Protein Gap Open Penalty = 10.0
  • Protein Gap Extension Penalty = 0.2
  • Protein matrix = Gonnet
  • Protein/DNA ENDGAP = -1
  • Protein/DNA GAPDIST = 4
How can I see the parameter values that are used by the ClustalW program?

If you submit your job by email, you will receive two emails. The first one is a confirmation mail that lists the parameters that you have chosen. The second mail contains a link to the ClustalW result page. It is not possible to show the submission parameters on the result page, because ClustalW does not include them in the ClustalW output.

How long are ClustalW results stored at the EBI?

If you run an interactive job, the results will be available for 24 hours. The results of an email job are available for 2 weeks. Some big files are removed after 15 minutes due to space constraints.

Does my job have an identifier?

Yes. You will find it on the results page. The job identifier has the job name, the date and a random number. If you want to report any errors or queries about a job, please tell us the job identifier.

Where can I download the ClustalW software from?

Both ClustalW and ClustalX can be downloaded from the EBI ftp site.
We do not distribute the CGI script for the web interface. The CGI.pm module (available from many perl sites on the internet) is needed to build a cgi interface for the command-line version of ClustalW.

How do I reference use of this service?

Chenna, Ramu, Sugawara, Hideaki, Koike,Tadashi, Lopez, Rodrigo, Gibson, Toby J, Higgins, Desmond G, Thompson, Julie D.
Multiple sequence alignment with the Clustal series of programs. (2003)
Nucleic Acids Res 31 (13):3497-500 PubMedID: 12824352

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ClustalW FAQ (Frequently Asked Questions)