Workflow Entry: Phylogenetic Study Using the Bio Extract Server

Created at: 17/06/10 @ 16:34:50      Last updated: 19/07/10 @ 20:00:00
Information Version 2 (latest) (of 2)
View version:

Version created on: 19/07/10 @ 19:56:36 by: Kendra Giesey   |   Revision comments Expand

Last edited on: 19/07/10 @ 20:00:00 by: Kendra Giesey

Title: Phylogenetic Study Using the Bio Extract Server

Type: BioExtract Server


Information Preview

(Click on the image to get the full size)

Medium


Information Description

This workflow, created using the BioExtract Server, contains a nucleotide query (using the NCBI Core Nucleotide Database), Blastn (against the Homo sapiens genome), Blastn (against the Mus musculus genome), the Format Conversion tool, the Fetch Translator Tool, and ClustalW. This workflow was created following the analytical steps described in the journal article "Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations" by Bjorn M Hallstrom and Axel Janke, published in BMC Evolutionary Biology. Although the workflow was based off of the study described in this article, it can be used in other experiments to find the phylogenetical distance between different genomes.

Note: In order to select specific sequences to be used in the workflow, the user must execute the workflow and then pause each of the two "blastn" steps before they begin. The user can then go to the "Extracts" tab and select the results that they would like to use. Once back in the "Extracts" tab, the "Execute/Resume" button at the top of the workflow must be clicked to resume the process.

 

Information Download



Information Run

Run this Workflow in the BioExtract Server...



Information Workflow Components

Not available

Information Workflow Type

BioExtract Server

Information Original Uploader

Information License

All versions of this Workflow are licensed under:

Information Credits (2)

(People/Groups)

Information Attributions (0)

(Workflows/Files)

None

Information Tags (4)

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Ratings (0)

Current:

0.0 / 5

(0 ratings)

Log in to rate and see breakdown of ratings

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

 

Citations (1)

1. Bjorn M Hallstrom and Axel Janke, Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations, BMC Evolutionary Biology, 27 May 2008, Accessed at: 24 May 2010


Version History

Earliest Version:
[1] - Phylogenetic Study Using the BioExtract Server

Created on: Thursday 17 June 2010 @ 16:34:50 (GMT)

Created by: Kendra Giesey

Revision comments:

None

Latest Version:
[2] - Phylogenetic Study Using the Bio Extract Server

Created on: Monday 19 July 2010 @ 19:56:36 (GMT)

Created by: Kendra Giesey

Last edited on: Monday 19 July 2010 @ 20:00:00 (GMT)

Last edited by: Kendra Giesey

Revision comments:

This version of the workflow contains the steps "Format Conversion" and "Fetch Translation" instead of the original "Transeq" step.



Reviews Reviews (0)

No reviews yet

Be the first to review!



Comments Comments (0)

No comments yet

Log in to make a comment




Workflow Other workflows that use similar services (0)

There are no workflows in myExperiment that use similar services to this Workflow.

What is this?

Linked Data

Non-Information Resource URI: http://www.myexperiment.org/workflows/1343


Alternative Formats

HTML
RDF
XML

New/Upload

Log in / Register

Username or Email:

Password:

Remember me:

OR

Use OpenID:


(eg: name.myopenid.com)

Need an account?
Click here to register

Forgot Password?

Front Page

Home

Invite people to myExperiment

Help pages

About Us

News and Events

Mailing List

Contact Us

Developers

Publications


Taverna Workflow Workbench

myGrid

BioCatalogue

Trident

Google Coop Search

EPSRC

JISC

Microsoft

Powered by:

Rails

Icons:
Silk icon set 1.3