EBI_ClustalW2_phylogentic_tree

Created: 2009-04-07 20:09:32

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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).

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Workflow Components

Inputs (2)

Name	Description
Sequence_alignment	A sequence alignment in an appropriate format (e.g. fasta, clustalw or MSF).
Email_address	User's 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
Contents_list	local
Input_data	local
Get_output	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#poll_jobid_type)
Get_phylip_tree_result	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#poll_jobid_type)
Unpack_output	local
Unpack_phylip_tree	local
Unpack_nj_tree	local
Get_nj_tree_result	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#poll_jobid_type)
EBI_ClustalW2_poll_job	workflow	Wait for job to finish.

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
Job_ID	EBI job identifier.
ClustalW_output	Output from the ClustalW program. Useful for diagnosing problems.
ClustalW_phylip_tree	The phylogenetic tree in PHYLIP format, for use with tree drawing tools.
ClustalW_nj_tree	Description of the tree.

Links (16)

Source	Sink
Contents_list:output	runClustalW2:content
Email_address	Job_params:email
Get_nj_tree_result:result	Unpack_nj_tree:bytes
Get_output:result	Unpack_output:bytes
Get_phylip_tree_result:result	Unpack_phylip_tree:bytes
Input_data:output	Contents_list:WSArrayofData
Job_params:output	runClustalW2:params
Sequence_alignment	Input_data:content
runClustalW2:jobid	EBI_ClustalW2_poll_job:Job_ID
Unpack_nj_tree:string	ClustalW_nj_tree
runClustalW2:jobid	Get_nj_tree_result:jobid
Unpack_output:string	ClustalW_output
Unpack_phylip_tree:string	ClustalW_phylip_tree
runClustalW2:jobid	Get_output:jobid
runClustalW2:jobid	Get_phylip_tree_result:jobid
runClustalW2:jobid	Job_ID

Coordinations (3)

Controller	Target
EBI_ClustalW2_poll_job	Get_output
EBI_ClustalW2_poll_job	Get_phylip_tree_result
EBI_ClustalW2_poll_job	Get_nj_tree_result

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Hamish McWilliam

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Hamish McWilliam

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EBI_ClustalW2_phylogentic_tree

Created by Hamish McWilliam on Saturday 31 May 2008 13:07:34 (UTC)
EBI_ClustalW2_phylogentic_tree

Created by Hamish McWilliam on Tuesday 07 April 2009 20:09:32 (UTC)

Revision comment:

Update for changes in web service message nomenclature.

Reviews (1)

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Cjmei7

Title: It works but how do I display the tree?

Rating: 4 out of 5

Created: 2010-04-08 17:22:26 | Updated: 2010-04-08 17:22:26

It works but how do I display the tree?

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Hamish McWilliam

The tree can be viewed using any tool which understands the Newick tree format. There are various tools in PHYLIP (http://evolution.genetics.washington.edu/phylip.html) which can be used to manipulate the tree and create images from it. Many of the PHYLIP tools are included in the Soaplab services (via the PHYLIPNEW EMBASSY package). Many interactive tools are also available, see http://evolution.gs.washington.edu/phylip/software.html#Interactive.

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 (2)

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Perform a ClustalW multiple sequence alignment using the EBI’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. Note: the WSClustalW2 service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement ClustalW2 servi...

Created: 2009-04-07 | Last updated: 2010-12-06

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