Table of Contents
Renaming notice! This tool will be renamed 'Simple Phylogeny' on 1st December. Existing functionality will remain identical, but we recommend migrating workflows to the simple_phylogeny as soon as it is available.
ClustalW 1) can generate Neighbor-joining 2) 3) or UPGMA 4) 5) 6) phylogentic trees from a multiple sequence alignment. This service separates the phylogeny features of ClustalW from the multiple sequence alignment functionality.
For more information see:
For Clustal multiple sequence alignment, see:
Web service registry entries:
We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of up to 30 at a time and to not submit more until the results and processing has completed for these. This enables users as well as the service maintainers to deal more easily with local and remote network outages as well as scheduled or unscheduled downtime.
Sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.
For further details of these tool-kits and workflow platforms see our Guide to Web Services.
The WSDL for the ClustalW2 Phylogeny (SOAP) service: http://www.ebi.ac.uk/Tools/services/soap/clustalw2_phylogeny?wsdl
Get a list of the parameter names.
Returns: a list of strings giving the names of the parameters.
Get details of a specific parameter.
Returns: a wsParameterDetails describing the parameter and its values.
Submit a job to the service.
Returns: a string containing the job identifier (
Get the status of a submitted job.
Returns: a string containing the status.
The values for the status are:
Further details can be found in Synchronous and Asynchronous Access: JDispatcher.
Get the available result types for a finished job.
Returns: a list of wsResultType data structures describing the available result types.
Get the result of a job of the specified type.
Returns: the result data for the specified type, base64 encoded. Depending on the SOAP library and programming language used the result may be returned in decoded form. For some result types (e.g. images) this will be binary data rather than a text string.
The input parameters for the job:
More detailed information about each parameter, including valid values can be obtained using the getParameterDetails(parameterId) operation.
Descriptive information about a tool parameter. Returned by getParameterDetails(parameterId).
Description of a tool parameter value. Used in wsParameterDetails.
Properties of a tool parameter value. Used in wsParameterValue.
Additional parameters passed when requesting a result. See getResult(jobId, type, parameters).
Description of a result type. Returned by getResultTypes(jobId).
1) Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J. and Higgins D.G. (2007)
Clustal W and Clustal X version 2.0.
2) Saitou N. and Nei. M. (1987)
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Mol. Evol. Biol 4(4):406-425
4) Sokal, R. and Michener, C. (1958)
A statistical method for evaluating systematic relationships
University of Kansas Science Bulletin 38:1409–1438.
5) Sneath P.H.A. and Sokal R.R. (1973)
Numerical taxonomy — the principles and practice of numerical classification.
(W. H. Freeman: San Francisco.)
7) Kimura, M. (1980)
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
Journal of Molecular Evolution 16:111–120.