clustal_phylogeny

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

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

Information Preview

Information Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/3370/download?version=2
[ More InfoExpand ]


Information Workflow Components

Information Authors (1)
Information Titles (1)
Information Descriptions (1)
Information Dependencies (0)
Inputs (2)
Processors (9)
Beanshells (0)
Outputs (2)
Datalinks (12)
Coordinations (1)

Information Workflow Type

Taverna 2

Information License

All versions of this Workflow are licensed under:

Information Version 2 (of 3)

View version:

Information Credits (1)

(People/Groups)

Information Attributions (0)

(Workflows/Files)

None

Information Tags (7)

Log in to add Tags

Information Shared with Groups (1)

Information Featured In Packs (1)

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

 

Citations (0)

None


Version History

In chronological order:



Reviews Reviews (0)

No reviews yet

Be the first to review!



Comments Comments (1)

Log in to make a comment

  • 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?




Workflow Other workflows that use similar services (1)

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

Thumb
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: User Stian Soiland-Reyes User Katy Wolstencroft

Attributions: Workflow Blast_Align_and_Tree