EBI_ClustalW2

Created: 2009-04-07 20:06:03 Last updated: 2010-12-06 11:00:19

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Perform a ClustalW multiple sequence alignment using the EBIâ€™s WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2). The set of sequences to align are the input, the other parameters for the search (see Job_params) are allowed to default.

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Workflow Components

Inputs (2)

Name	Description
Sequences	Sequences to align (fasta format recommended).
Email_address	User e-mail address.

Processors (11)

Name	Type	Description
runClustalW2	arbitrarywsdl	Submit a ClustalW analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#runclustalw2_params_content)
Job_params	local
Content_list	local
Input_data	local
Get_alignment_result	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#poll_jobid_type)
Get_guide_tree_result	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#poll_jobid_type)
Unpack_alignment_result	local
Unpack_guide_tree_result	local
EBI_ClustalW2_poll_job	workflow	Check for job status, and wait if job not finished.
Get_output_result	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#poll_jobid_type)
Unpack_output_result	local

Beanshells (1)

Name	Description	Inputs	Outputs
Is_done	Map job status into true/false is done flag	job_status	is_done

Outputs (4)

Name	Description
ClustalW_alignment	The alignment in ClustalW format.
ClustalW_guide_tree	Guide tree used to produce the final alignment.
Job_ID	EBI job identifier
ClustalW_output

Links (16)

Source	Sink
Email_address	Job_params:email
Content_list:output	runClustalW2:content
Get_alignment_result:output	Unpack_alignment_result:bytes
Get_guide_tree_result:output	Unpack_guide_tree_result:bytes
Get_output_result:output	Unpack_output_result:bytes
Input_data:output	Content_list:WSArrayofData
Job_params:output	runClustalW2:params
Sequences	Input_data:content
Unpack_alignment_result:string	ClustalW_alignment
Unpack_guide_tree_result:string	ClustalW_guide_tree
Unpack_output_result:string	ClustalW_output
runClustalW2:jobid	EBI_ClustalW2_poll_job:Job_ID
runClustalW2:jobid	Get_alignment_result:jobid
runClustalW2:jobid	Get_guide_tree_result:jobid
runClustalW2:jobid	Get_output_result:jobid
runClustalW2:jobid	Job_ID

Coordinations (3)

Controller	Target
EBI_ClustalW2_poll_job	Get_alignment_result
EBI_ClustalW2_poll_job	Get_guide_tree_result
EBI_ClustalW2_poll_job	Get_output_result

Information Workflow Type

Taverna 1

Information Uploader

Hamish McWilliam

Information License

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Information Version 1 (earliest) (of 2)

Information Credits (1)

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Hamish McWilliam

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Information Featured In Packs (2)

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EMBL-EBI Web Services (retired)

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Information Attributed By (5)

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Information Statistics

6705 viewings

3461 downloads

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Version History

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EBI_ClustalW2

Created by Hamish McWilliam on Saturday 31 May 2008 10:27:58 (UTC)

Last edited by Hamish McWilliam on Monday 02 June 2008 21:27:39 (UTC)
EBI_ClustalW2

Created by Hamish McWilliam on Tuesday 07 April 2009 20:06:03 (UTC)

Last edited by Hamish McWilliam on Monday 06 December 2010 11:00:19 (UTC)

Revision comment:

Update for changes in nomenclature used in web service.

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Other workflows that use similar services (7)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 1

Uploader

Hamish McWilliam

EBI_ClustalW2_phylogentic_tree (2)

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Create a Neighbor-joining phylogenetic tree, with Kimura distance corrections, from a sequence alignment using the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2).

Created: 2009-04-07

Credits: Hamish McWilliam

Taverna 1

Uploader

Hamish McWilliam

EBI_ClustalW_alignment_tree (2)

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Given a set of sequences perform an multiple sequence alignment and from the multiple alignment derive a phylogenetic tree. The popular ClustalW program (see http://www.clustal.org/), as implemented in the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2) is used to perform both tasks.

Created: 2008-05-31 | Last updated: 2010-12-03

Credits: Hamish McWilliam

Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree