Research Article

No access

Published Online: 10 August 2006

Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)

Publication: OMICS:A Journal of Integrative Biology

Volume 10, Issue Number 2

https://doi.org/10.1089/omi.2006.10.231

Permissions & Citations

Abstract

In the eight years since phylogenomics was introduced as the intersection of genomics and phylogenetics, the field has provided fundamental insights into gene function, genome history and organismal relationships. The utility of phylogenomics is growing with the increase in the number and diversity of taxa for which whole genome and large transcriptome sequence sets are being generated. We assert that the synergy between genomic and phylogenetic perspectives in comparative biology would be enhanced by the development and refinement of minimal reporting standards for phylogenetic analyses. Encouraged by the development of the Minimum Information About a Microarray Experiment (MIAME) standard, we propose a similar roadmap for the development of a Minimal Information About a Phylogenetic Analysis (MIAPA) standard. Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors.

This paper is part of the special issue of OMICS on data standards.

Get full access to this article

View all available purchase options and get full access to this article.

Information & Authors

Information

Published In

cover image OMICS: A Journal of Integrative Biology

OMICS:A Journal of Integrative Biology

Volume 10 • Issue Number 2 • June 2006

Pages: 231 - 237

PubMed: 16901231

Copyright

Copyright 2006, Mary Ann Liebert, Inc.

History

Published online: 10 August 2006

Published in print: June 2006

Permissions

Request permissions for this article.

Request Permissions

Topics

Authors

Affiliations

Dr. Jim Leebens-Mack

Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania.

New address: Department of Plant Biology, University of Georgia, Athens, Georgia 30602.

View all articles by this author

Todd Vision

Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.

View all articles by this author

Eric Brenner

New York Botanical Garden, Bronx, New York.

View all articles by this author

John E. Bowers

Applied Genetic Technology Center, Departments of Crop and Soil Science, Botany, and Genetics, University of Georgia, Athens, Georgia.

View all articles by this author

Steven Cannon

USDA-ARS, and Department of Agronomy, Iowa State University, Ames, Iowa.

View all articles by this author

Mark J. Clement

Networked Computing Laboratory, Computer Science Department, Brigham Young University, Provo, Utah.

View all articles by this author

Clifford W. Cunningham

Department of Biology, Duke University, Durham, North Carolina.

View all articles by this author

Claude DePamphilis

Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania.

View all articles by this author

Rob DeSalle

Division of Invertebrate Zoology, American Museum of Natural History, New York, New York.

View all articles by this author

Jeff J. Doyle

L.H. Bailey Hortorium, Cornell University, Ithaca, New York.

View all articles by this author

Jonathan A. Eisen

UC Davis Genome Center, Section of Evolution and Ecology, and the Department of Medical Microbiology and Immunology, University of California, Davis, California.

View all articles by this author

Xun Gu

Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa.

View all articles by this author

John Harshman

Pepperwood Way, San Jose, California.

View all articles by this author

Robert K. Jansen

Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas.

View all articles by this author

Elizabeth A. Kellogg

Department of Biology, University of Missouri, Saint Louis, Missouri.

View all articles by this author

Eugene V. Koonin

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland.

View all articles by this author

Brent D. Mishler

University Herbarium, Jepson Herbarium, and Department of Integrative Biology, University of California, Berkeley, California.

View all articles by this author

Hervé Philippe

Canadian Institute for Advanced Research, Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, Succursale Centre-Ville, Montreal, Canada.

View all articles by this author

J. Chris Pires

Division of Biological Sciences, University of Missouri—Columbia, Columbia, Missouri.

View all articles by this author

Yin-Long Qiu

Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan.

View all articles by this author

Seung Y. Rhee

Department of Plant Biology, Carnegie Institution, Stanford, California.

View all articles by this author

Kimmen Sjölander

Department of Bioengineering, University of California, Berkeley, California.

View all articles by this author

Douglas E. Soltis

Department of Botany and the Genetics Institute, University of Florida, Gainesville, Florida.

View all articles by this author

Pamela S. Soltis

Florida Museum of Natural History and the Genetics Institute, University of Florida, Gainesville, Florida.

View all articles by this author

Dennis W. Stevenson

New York Botanical Garden, Bronx, New York.

View all articles by this author

Kerr Wall

Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania.

View all articles by this author

Tandy Warnow

Department of Computer Science, University of Texas at Austin, Austin, Texas.

View all articles by this author

Christian Zmasek

Burnham Institute for Medical Research, La Jolla, California.

View all articles by this author

Metrics & Citations

Metrics

Citations

Export citation

Select the format you want to export the citations of this publication.

View Options

Access content

To read the fulltext, please use one of the options below to sign in or purchase access.

Purchase Save for later

Article Pay Per View Purchase: 24 hours to view or download: OMI $51.00 Add to cart

⚠ Society Access

If you are a member of a society that has access to this content please log in via your society website and then return to this publication.

Restore your content access

Note: This functionality works only for purchases done as a guest. If you already have an account, log in to access the content to which you are entitled.

View options

PDF/EPUB

Figures

Tables

Media

Topics

Back to Top