Phylogenetic analysis with the iPlant discovery environment

Matasci, N., McKay, S. (June 2013) Phylogenetic analysis with the iPlant discovery environment. Current protocols in bioinformatics (SUPPL.). 6.13.1-6.13.13. ISSN 19343396 (ISSN)

URL: http://www.ncbi.nlm.nih.gov/pubmed/23749754
DOI: 10.1002/0471250953.bi0613s42

Abstract

The iPlant Collaborative's Discovery Environment is a unified Web portal to many bioinformatics applications and analytical workflows, including various methods of phylogenetic analysis. This unit describes example protocols for phylogenetic analyses, starting at sequence retrieval from the GenBank sequence database, through to multiple sequence alignment inference and visualization of phylogenetic trees. Methods for extracting smaller sub-trees from very large phylogenies, and the comparative method of continuous ancestral character state reconstruction based on observed morphology of extant species related to their phylogenetic relationships, are also presented. © 2013 by John Wiley & Sons, Inc.

Item Type: Paper
Uncontrolled Keywords: Continuous ancestral character estimation Maximum likelihood Multiple sequence alignment Phylogenetics
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
educational material
CSHL Authors:
Communities: Dolan DNA Learning Center
Depositing User: Matt Covey
Date: 1 June 2013
Date Deposited: 20 Sep 2013 14:02
Last Modified: 20 Sep 2013 14:02
Related URLs:
URI: http://repository.cshl.edu/id/eprint/28567

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