Table of Contents
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 WADL for the ClustalW2 Phylogeny (REST) service: http://www.ebi.ac.uk/Tools/services/rest/clustalw2_phylogeny?wadl
List parameter names.
An XML document containing a list of parameter names.
Get detailed information about a parameter.
An XML document providing details about the parameter.
Submit a job with the specified parameters.
More detailed information about each parameter, including valid values can be obtained using the getParameterDetails(parameterId) operation.
A plain text document containing the job identifier.
Get the status of a submitted job.
A plain text document containing the job status.
The values for the status are:
Further details can be found in Synchronous and Asynchronous Access: JDispatcher.
Get available result types for a finished job.
An XML document detailing the available result types.
Get the job result of the specified type.
A document containing the result in the requested format. The MIME type of the returned document is set according to the format.
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.