Taking the first steps towards a standard for reporting on phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)

Jim Leebens-Mack, Todd Vision, Eric Brenner, John E. Bowers, Steven Cannon, Mark J. Clement, Clifford W. Cunningham, Claude DePamphilis, Rob DeSalle, Jeff J. Doyle, Jonathan A. Eisen, Xun Gu, John Harshman, Robert K. Jansen, Elizabeth A. Kellogg, Eugene V. Koonin, Brent D. Mishler, Hervé Philippe, J. Chris Pires, Yin Long QiuSeung Y. Rhee, Kimmen Sjölander, Douglas E. Soltis, Pamela S. Soltis, Dennis W. Stevenson, Kerr Wall, Tandy Warnow, Christian Zmasek

Research output: Contribution to journalReview article

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.

Original languageEnglish (US)
Pages (from-to)231-237
Number of pages7
JournalOMICS A Journal of Integrative Biology
Volume10
Issue number2
DOIs
StatePublished - Sep 4 2006
Externally publishedYes

Fingerprint

Phylogeny
Genes
Genome
Microarrays
Genomics
Transcriptome
Software
Databases
Experiments

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Genetics

Cite this

Taking the first steps towards a standard for reporting on phylogenies : Minimum Information about a Phylogenetic Analysis (MIAPA). / Leebens-Mack, Jim; Vision, Todd; Brenner, Eric; Bowers, John E.; Cannon, Steven; Clement, Mark J.; Cunningham, Clifford W.; DePamphilis, Claude; DeSalle, Rob; Doyle, Jeff J.; Eisen, Jonathan A.; Gu, Xun; Harshman, John; Jansen, Robert K.; Kellogg, Elizabeth A.; Koonin, Eugene V.; Mishler, Brent D.; Philippe, Hervé; Pires, J. Chris; Qiu, Yin Long; Rhee, Seung Y.; Sjölander, Kimmen; Soltis, Douglas E.; Soltis, Pamela S.; Stevenson, Dennis W.; Wall, Kerr; Warnow, Tandy; Zmasek, Christian.

In: OMICS A Journal of Integrative Biology, Vol. 10, No. 2, 04.09.2006, p. 231-237.

Research output: Contribution to journalReview article

Leebens-Mack, J, Vision, T, Brenner, E, Bowers, JE, Cannon, S, Clement, MJ, Cunningham, CW, DePamphilis, C, DeSalle, R, Doyle, JJ, Eisen, JA, Gu, X, Harshman, J, Jansen, RK, Kellogg, EA, Koonin, EV, Mishler, BD, Philippe, H, Pires, JC, Qiu, YL, Rhee, SY, Sjölander, K, Soltis, DE, Soltis, PS, Stevenson, DW, Wall, K, Warnow, T & Zmasek, C 2006, 'Taking the first steps towards a standard for reporting on phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)', OMICS A Journal of Integrative Biology, vol. 10, no. 2, pp. 231-237. https://doi.org/10.1089/omi.2006.10.231
Leebens-Mack, Jim ; Vision, Todd ; Brenner, Eric ; Bowers, John E. ; Cannon, Steven ; Clement, Mark J. ; Cunningham, Clifford W. ; DePamphilis, Claude ; DeSalle, Rob ; Doyle, Jeff J. ; Eisen, Jonathan A. ; Gu, Xun ; Harshman, John ; Jansen, Robert K. ; Kellogg, Elizabeth A. ; Koonin, Eugene V. ; Mishler, Brent D. ; Philippe, Hervé ; Pires, J. Chris ; Qiu, Yin Long ; Rhee, Seung Y. ; Sjölander, Kimmen ; Soltis, Douglas E. ; Soltis, Pamela S. ; Stevenson, Dennis W. ; Wall, Kerr ; Warnow, Tandy ; Zmasek, Christian. / Taking the first steps towards a standard for reporting on phylogenies : Minimum Information about a Phylogenetic Analysis (MIAPA). In: OMICS A Journal of Integrative Biology. 2006 ; Vol. 10, No. 2. pp. 231-237.
@article{92fcb015521b4f8d9c73cafb56c85a1d,
title = "Taking the first steps towards a standard for reporting on phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)",
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.",
author = "Jim Leebens-Mack and Todd Vision and Eric Brenner and Bowers, {John E.} and Steven Cannon and Clement, {Mark J.} and Cunningham, {Clifford W.} and Claude DePamphilis and Rob DeSalle and Doyle, {Jeff J.} and Eisen, {Jonathan A.} and Xun Gu and John Harshman and Jansen, {Robert K.} and Kellogg, {Elizabeth A.} and Koonin, {Eugene V.} and Mishler, {Brent D.} and Herv{\'e} Philippe and Pires, {J. Chris} and Qiu, {Yin Long} and Rhee, {Seung Y.} and Kimmen Sj{\"o}lander and Soltis, {Douglas E.} and Soltis, {Pamela S.} and Stevenson, {Dennis W.} and Kerr Wall and Tandy Warnow and Christian Zmasek",
year = "2006",
month = "9",
day = "4",
doi = "10.1089/omi.2006.10.231",
language = "English (US)",
volume = "10",
pages = "231--237",
journal = "OMICS A Journal of Integrative Biology",
issn = "1536-2310",
publisher = "Mary Ann Liebert Inc.",
number = "2",

}

TY - JOUR

T1 - Taking the first steps towards a standard for reporting on phylogenies

T2 - Minimum Information about a Phylogenetic Analysis (MIAPA)

AU - Leebens-Mack, Jim

AU - Vision, Todd

AU - Brenner, Eric

AU - Bowers, John E.

AU - Cannon, Steven

AU - Clement, Mark J.

AU - Cunningham, Clifford W.

AU - DePamphilis, Claude

AU - DeSalle, Rob

AU - Doyle, Jeff J.

AU - Eisen, Jonathan A.

AU - Gu, Xun

AU - Harshman, John

AU - Jansen, Robert K.

AU - Kellogg, Elizabeth A.

AU - Koonin, Eugene V.

AU - Mishler, Brent D.

AU - Philippe, Hervé

AU - Pires, J. Chris

AU - Qiu, Yin Long

AU - Rhee, Seung Y.

AU - Sjölander, Kimmen

AU - Soltis, Douglas E.

AU - Soltis, Pamela S.

AU - Stevenson, Dennis W.

AU - Wall, Kerr

AU - Warnow, Tandy

AU - Zmasek, Christian

PY - 2006/9/4

Y1 - 2006/9/4

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=33748032715&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33748032715&partnerID=8YFLogxK

U2 - 10.1089/omi.2006.10.231

DO - 10.1089/omi.2006.10.231

M3 - Review article

C2 - 16901231

AN - SCOPUS:33748032715

VL - 10

SP - 231

EP - 237

JO - OMICS A Journal of Integrative Biology

JF - OMICS A Journal of Integrative Biology

SN - 1536-2310

IS - 2

ER -