This document discusses standards and resources for reporting on phylogenetic analyses. It outlines the minimum information that should be included when publishing results of phylogenetic studies, such as character matrices, phylogenetic methods and analysis parameters, and links to external resources. It also reviews existing standards and formats for phylogenetic data, including TreeBASE, DRYAD, NeXML, and the CDAO ontology. Current related efforts within organizations like TDWG are also mentioned.

1. Objectives of larger phylogenetic
study and component trees
Character
states
Character Matrix
Phylogeny
Procedures for
establishing
homologies
Phylogenetic
methods and
analysis parameters
External resources Publication
(e.g. PubMed)
Character
database
(e.g.
GenBank,
morphbank,
MorphBank)
MIAPA
Taxonomic
database
Specimen
Information
Voucher
Information
MIAPA: Minimum Information about a Phylogenetic Analysis

2. • Initial publication: Leebens-Mack et al. 2006. Taking the First Steps
towards a Standard for Reporting on Phylogenies: Minimum
Information about a Phylogenetic Analysis (MIAPA). OMICS, 10(2):
231-237.
• TreeBASE and DRYAD: Prototype and de facto minimum standards
• PhyloWS: An emerging API specification for web-services;
programmable and predictable interface to on-line phylogenetic
database.
• Exchange formats and computable semantics:
– NEXUS: Legacy exchange format
– NeXML: Phylogenetic character data and trees expressed in XML
– CDAO: Ontology for evolutionary biology
– JSON?
• Phyloinformatics in TDWG (Taxonomic Database Working Group)
Status

3. Brent D. Mishler
Christian Zmasek
Claude Depamphilis
Clifford W. Cunningham
Dennis W. Stevenson
Douglas E. Soltis
Elizabeth A. Kellogg
Eric Brenner
Eugene V. Koonin
Herveé Philippe
J. Chris Pires
Jeff J. Doyle
Jim Leebens-Mack
John E. Bowers
John Harshman
Jonathan A. Eisen
Kerr Wall
Kimmen Sjölander
Mark J. Clement
Pamela S. Soltis
Rob DeSalle
Robert K. Jansen
Seung Y. Rhee
Steven Cannon
Tandy Warnow
Todd Vision
Xun Gu
Yin-Long Qiu
Community Support (Initial Publication)
Karen Cranston
Michael Donoghue
Rob Guralnick
David Maddison
William Piel
Val Tannen
Rutger Vos
Mark Westneat
PRF, Inc (TreeBASE)
NESCent
CDAO
NeXML
DRYAD
pPOD
TDWG
Interested Parties
Organizations