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ClustalW2 Phylogeny (REST)

Description

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:

Important

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.

Service provision happens on a fair-share basis. Overzealous usage of a particular resource will be dealt with in accordance to the EMBL-EBI's Terms of Use.

Clients

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
Perl clustalw2phylogeny_lwp.pl LWP and XML::Simple

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

WADL

The WADL for the ClustalW2 Phylogeny (REST) service: http://www.ebi.ac.uk/Tools/services/rest/clustalw2_phylogeny?wadl

Resources

parameters

List parameter names.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/clustalw2_phylogeny/parameters/
Parameters none

Response

An XML document containing a list of parameter names.

For example: http://www.ebi.ac.uk/Tools/services/rest/clustalw2_phylogeny/parameters/

parameterdetails

Get detailed information about a parameter.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/clustalw2_phylogeny/parameterdetails/$parameterId
Parameters $parameterId: the name of the parameter

Response

An XML document providing details about the parameter.

For example: http://www.ebi.ac.uk/Tools/services/rest/clustalw2_phylogeny/parameterdetails/clustering.

run

Submit a job with the specified parameters.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/clustalw2_phylogeny/run/
POST email User e-mail address. See Why do you need my e-mail address?
title an optional title for the job.
tree output format for tree
kimura use Kimura's distance correction 7) 8)
tossgaps exclude columns containing gaps from distance
clustering clustering method used to generate tree
pim output percentage identify matrix for sequences
sequence aligned sequences

More detailed information about each parameter, including valid values can be obtained using the getParameterDetails(parameterId) operation.

Response

A plain text document containing the job identifier.

status

Get the status of a submitted job.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/clustalw2_phylogeny/status/$jobId
Parameters $jobId: job identifier

Response

A plain text document containing the job 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.

resulttypes

Get available result types for a finished job.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/clustalw2_phylogeny/resulttypes/$jobId
Parameters $jobId: job identifier

Response

An XML document detailing the available result types.

result

Get the job result of the specified type.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/clustalw2_phylogeny/result/$jobId/$resultType
Parameters $jobId: job identifier
$resultType: type of result to retrieve. See resulttypes.

Response

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.
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_rest.txt · Last modified: 2014/09/07 08:53 by uludag
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