ClustalW2 Phylogeny (SOAP)


This service has been renamed 'Simple Phylogeny'. Please migrate your processes to use the new simple phylogeny web service as soon as possible as the clustalw_phylogeny service will be retired.

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 no more than 30 at a time and not to submit more until the results and processing is complete. Please ensure that a valid email address is provided. Excessive usage of a particular resource will be dealt with in accordance with EMBL-EBI's Terms of Use. Please contact us if you need further information.


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.

Language Download Requirements
C# .NET Executable: ClustalW2PhylogenyCliClient.exe; Source: AbstractWsClient.cs, ClustalW2PhylogenyClient.cs, ClustalW2PhylogenyCliClient.cs A .NET runtime environment. If building from source development tools are also required. See the .NET tutorial for details.
Java Executable jar: ClustalW2Phylogeny_Axis1.jar; Source:, Axis 1.4; All dependencies, including Axis 1.4 and Commons-CLI, are available in
Perl SOAP::Lite

For further details of these tool-kits and workflow platforms see our Guide to Web Services.


The WSDL for the ClustalW2 Phylogeny (SOAP) service:



Get a list of the parameter names.

Arguments: none

Returns: a list of strings giving the names of the parameters.


Get details of a specific parameter.


  • parameterId: identifier/name of the parameter to fetch details of.

Returns: a wsParameterDetails describing the parameter and its values.

run(email, title, params)

Submit a job to the service.


Returns: a string containing the job identifier (jobId).


Get the status of a submitted job.


  • jobId: (required) job identifier.

Returns: a string containing the status.

The values for the status are:

  • RUNNING: the job is currently being processed.
  • FINISHED: job has finished, and the results can then be retrieved.
  • ERROR: an error occurred attempting to get the job status.
  • FAILURE: the job failed.
  • NOT_FOUND: the job cannot be found.

Further details can be found in Synchronous and Asynchronous Access: JDispatcher.


Get the available result types for a finished job.


  • jobId: (required) job identifier.

Returns: a list of wsResultType data structures describing the available result types.

getResult(jobId, type, parameters)

Get the result of a job of the specified type.


  • jobId: (required) job identifier.
  • type: (required) string specifying the result type to fetch. See getResultTypes(jobId) for details of the available types.
  • parameters: optional list of wsRawOutputParameter used to provide additional parameters for derived result types.

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.

Data Types


The input parameters for the job:

Attribute Type Description
tree string output format for tree
kimura boolean use Kimura's distance correction 7) 8)
tossgaps boolean exclude columns containing gaps from distance
clustering string clustering method used to generate tree
pim boolean output percentage identify matrix for sequences
sequence string aligned sequences

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).

Attribute Type Description
name string Name of the parameter.
description string Description of the parameter, suitable for use in option help interfaces.
type string Data type of the parameter.
values list of wsParameterValue List of valid values for the option.


Description of a tool parameter value. Used in wsParameterDetails.

Attribute Type Description
label string Display name of the value, for use in interfaces.
value string String representation of the value to be passed to the tool parameter.
defaultValue boolean Flag indicating if this value is the default.
properties list of wsProperty List of key/value pairs providing further information.


Properties of a tool parameter value. Used in wsParameterValue.

Attribute Type Description
key string
value string


Additional parameters passed when requesting a result. See getResult(jobId, type, parameters).

Attribute Type Description
name string
value list of string


Description of a result type. Returned by getResultTypes(jobId).

Attribute Type Description
identifier string Identifier for the result type. Passed as type to getResult(jobId, type, parameters).
label string Display name for use in user interfaces.
description string Description of the result type, for use in help interfaces.
mediaType string MIME type of the returned data.
fileSuffix string Suggested suffix for file name, if writing data to disk.
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.
Bioinformatics 23(21):2947-8
PubMed: 17846036
DOI: 10.1093/bioinformatics/btm404
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
PubMed: 3447015
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.
PubMed: 7463489
DOI: 10.1007/BF01731581
services/phylogeny/clustalw2_phylogeny_soap.txt · Last modified: 2017/02/17 09:57 by apc