clustal_phylogeny

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

Download Workflow

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

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/3370/download?version=1
[ More Info Expand ]

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)

(People/Groups)

Katy Wolstencroft

Information Attributions (0)

(Workflows/Files)

None

Information Tags (7)

Uploader tags

Log in to add Tags

Information Shared with Groups (1)

NARExamples

Information Featured In Packs (1)

Bioinformatics Workflow Examples

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

2444 viewings

1329 downloads

[ see breakdown ]

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)

Reviews (0)

No reviews yet

Be the first to review!

Comments (1)

View Timeline

Log in to make a comment

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)

Download

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