clustal_phylogeny

Created: 2013-01-28 09:02:03 Last updated: 2013-03-11 15:26:43

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This workflow accepts a ClustalW protein sequence alignment and produces a phylogenetic tree, using the EBI clustalw_phylogeny web service, which implements phylip.

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (2)

Name	Description
alignment	accepts a clustalw protein sequence alignment
email	Requires a valid email address in order to execute services hosted at the EBI. The EBI asks for an email address so that they can contact you about: Problems with the service which affect your jobs. Scheduled maintenance which affects services you are using. Deprecation and retirement of a service you are using. If you use a fake email, the workflow may be cancelled before execution

Processors (9)

Name	Type	Description
run	wsdl	Wsdl http://www.ebi.ac.uk/Tools/services/soap/clustalw2_phylogeny?wsdl Wsdl Operation run
run_input	xmlsplitter
run_output	xmlsplitter
run_input_2	xmlsplitter
status	workflow
getResult	wsdl	Wsdl http://www.ebi.ac.uk/Tools/services/soap/clustalw2_phylogeny?wsdl Wsdl Operation getResult
getResult_input	xmlsplitter
type_value	stringconstant	Value tree
getResult_output	xmlsplitter

Beanshells (0)

Outputs (2)

Name	Description
status_report
getResult_output_output

Datalinks (12)

Source	Sink
run_input:output	run:parameters
run_input_2:output	run_input:parameters
email	run_input:email
run:parameters	run_output:input
alignment	run_input_2:sequence
run_output:jobId	status:JOB_ID
getResult_input:output	getResult:parameters
type_value:value	getResult_input:type
run_output:jobId	getResult_input:jobId
getResult:parameters	getResult_output:input
status:status	status_report
getResult_output:output	getResult_output_output

Coordinations (1)

Controller	Target
status	getResult_input

Information Workflow Type

Taverna 2

Information Uploader

Katy Wolstencroft

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 3)

Information Credits (1)

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Katy Wolstencroft

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None

Information Tags (7)

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Information Statistics

2408 viewings

1297 downloads

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Citations (0)

None

Version History

In chronological order:

clustal_phylogeny

Created by Katy Wolstencroft on Monday 28 January 2013 09:02:03 (UTC)
clustal_phylogeny

Created by Katy Wolstencroft on Tuesday 29 January 2013 12:18:43 (UTC)
clustal_phylogeny

Created by Katy Wolstencroft on Wednesday 30 January 2013 13:15:19 (UTC)

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Comments (1)

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Magnus Palmblad	Monday 11 March 2013 15:29:15 (UTC)
	Very nice and clearly documented workflow. I managed to generate a tree in Phylip. However, the MEGA format converter requires more information I think. Perhaps it would also be possible to draw the tree directly in the workflow, for instance using R-Phylo (http://www.r-phylo.org/wiki/Main_Page) in an Rshell component?

Other workflows that use similar services (1)

Taverna 2

Uploader

Stian Soiland-Reyes

Find compounds pharmacology and align agai... (1)

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Look up concept URI from freetext, e.g. "aspirin", find compound pharmacology and their target info. For each target, blast+tree on its sequence - if any. Uses the Open PHACTs API https://dev.openphacts.org/docs/alpha and the myExperiment workflow 3369 "Blast_Align_and_Tree" http://www.myexperiment.org/workflows/3369. Notice that in tihs workflow, most concepts won't have compounds, and most compounds won't have targets, and most targets won't have a sequence - Open PHACT API wise this mean...

Created: 2013-10-16

Credits: Stian Soiland-Reyes Katy Wolstencroft

Attributions: Blast_Align_and_Tree