Phylogenetic Analysis with the iPlant Discovery Environment

Naim Matasci1, Sheldon McKay2

1 The University of Arizona, Tucson, Arizona, 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 6.13
DOI:  10.1002/0471250953.bi0613s42
Online Posting Date:  June, 2013
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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.

Keywords: phylogenetics; maximum likelihood; continuous ancestral character estimation; multiple sequence alignment

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Table of Contents

  • Introduction
  • Basic Protocol 1: Building a Phylogenetic Tree Using Sequence Similarity
  • Alternate Protocol 1: Extracting Subtrees from a “Tree of Life”
  • Basic Protocol 2: Ancestral Character State Reconstuction for Continuous Traits
  • Support Protocol 1: Example File Download
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

   Ackerly, D. 2009. Colloquium Papers: Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal. Proc. Natl. Acad. Sci. U.S.A. 106:19699‐19706.
   Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI‐BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389‐3402.
   Benson, D.A., Karsch‐Mizrachi, I., Lipman, D.J., Ostell, J., and Sayers, E.W. 2011. GenBank. Nucleic Acids Res. 39:D32‐D37.
   Delsuc, F., Brinkmann, H., and Philippe, H. 2005. Phylogenomics and the reconstruction of the tree of life. Nature Rev. Genet. 6:361‐375.
   Edgar, R.C. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792‐1797.
   Goff, S.A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A.E., Gessler, D., Matasci, N., Wang, L., Hanlon, M., Lenards, A., Muir, A., Merchant, N., Lowry, S., Mock, S., Helmke, M., Kubach, A., Narro, M., Hopkins, N., Micklos, D., Hilgert, U., Gonzales, M., Jordan, C., Skidmore, E., Dooley, R., Cazes, J., McLay, R., Lu, Z., Pasternak, S., Koesterke, L., Piel, W.H., Grene, R., Noutsos, C., Gendler, K., Feng, X., Tang, C., Lent, M., Kim, S.J., Kvilekval, K., Manjunath, B.S., Tannen, V., Stamatakis, A., Sanderson, M., Welch, S.M., Cranston, K.A., Soltis, P., Soltis, D., O'Meara, B., Ane, C., Brutnell, T., Kleibenstein, D.J., White, J.W., Leebens‐Mack, J., Donoghue, M.J., Spalding, E.P., Vision, T.J., Myers, C.R., Lowenthal, D., Enquist, B.J., Boyle, B., Akoglu, A., Andrews, G., Ram, S., Ware, D., Stein, L., and Stanzione, D. 2011. The iPlant collaborative: Cyberinfrastructure for plant biology. Front. Plant Sci. 2:34.
   Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J., and Higgins, D.G. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947‐2948.
   Paradis, E., Claude, J., and Strimmer, K. 2004. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20:289‐290.
   Smith, S.A., Beaulieu, J.M., Stamatakis, A., and Donoghue, M.J. 2011. Understanding angiosperm diversification using small and large phylogenetic trees. Am. J. Botany 98:404‐414.
   Stamatakis, A., Aberer, A.J., Goll, C., Smith, S.A., Berger, S.A., and Izquierdo‐Carrasco, F. 2012. RAxML‐Light: A tool for computing terabyte phylogenies. Bioinformatics 28:2064‐2066.
   Stoltzfus, A., O'Meara, B., Whitacre, J., Mounce, R., Gillespie, E.L., Kumar, S., Rosauer, D.F., and Vos, R.A. 2012. Sharing and re‐use of phylogenetic trees (and associated data) to facilitate synthesis. BMC Res. Notes 5:574.
   Stoltzfus, A., Lapp, H., Matasci, N., Deus, H., Sidlauskas, B., Zmasek, C.M., Vaidya, G., Pontelli, E., Cranston, K., Vos, R.A., et al. Phylotastic! Making tree‐of‐life knowledge accessible, reusable and convenient. BMC Bioinformatics. In press.
   Wheeler, T. 2009. Large‐scale neighbor‐joining with NINJA. In Algorithms in Bioinformatics (S. Salzberg and T. Warnow, eds.) pp. 375‐389. Springer, Berlin.
Key Reference
   Goff et al., 2011. See above.
  Provides a complete overview of the iPlant Collaborative project.
Internet Resources
  iPlant Home page.
  iPlant Discovery Environment.
  NCBI GenBank sequence repository.
  MUSCLE Home page.
  RAxML Home page.
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