UNIT 6.13 Phylogenetic Analysis with the iPlant Discovery Environment

  1. Naim Matasci1,2,
  2. Sheldon McKay1,3

Published Online: 1 JUN 2013

DOI: 10.1002/0471250953.bi0613s42

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Matasci, N. and McKay, S. 2013. Phylogenetic Analysis with the iPlant Discovery Environment. Current Protocols in Bioinformatics. 42:6.13:6.13.1–6.13.13.

Author Information

  1. 1

    The iPlant Collaborative

  2. 2

    The University of Arizona, Tucson, Arizona

  3. 3

    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York

Publication History

  1. Published Online: 1 JUN 2013


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. Curr. Protoc. Bioinform. 42:6.13.1-6.13.13. © 2013 by John Wiley & Sons, Inc.


  • phylogenetics;
  • maximum likelihood;
  • continuous ancestral character estimation;
  • multiple sequence alignment