Extended Newick: it is time for a standard representation of phylogenetic networks
Open Access
- 15 December 2008
- journal article
- Published by Springer Science and Business Media LLC in BMC Bioinformatics
- Vol. 9 (1), 532
- https://doi.org/10.1186/1471-2105-9-532
Abstract
Phylogenetic trees resulting from molecular phylogenetic analysis are available in Newick format from specialized databases but when it comes to phylogenetic networks, which provide an explicit representation of reticulate evolutionary events such as recombination, hybridization or lateral gene transfer, the lack of a standard format for their representation has hindered the publication of explicit phylogenetic networks in the specialized literature and their incorporation in specialized databases. Two different proposals to represent phylogenetic networks exist: as a single Newick string (where each hybrid node is splitted once for each parent) or as a set of Newick strings (one for each hybrid node plus another one for the phylogenetic network). The standard we advocate as extended Newick format describes a whole phylogenetic network with k hybrid nodes as a single Newick string with k repeated nodes, and this representation is unique once the phylogenetic network is drawn or the ordering among children nodes is fixed. The extended Newick format facilitates phylogenetic data sharing and exchange, and also allows for the practical use of phylogenetic networks in computer programs and scripts. This standard has been recently agreed upon by a number of computational biologists, is already supported by several phylogenetic tools, and avoids the different drawbacks of using an a priori unknown number of Newick strings without any additional mark-up to represent a phylogenetic network. The adoption of the extended Newick format as a standard for the representation of phylogenetic network is an important step towards the publication of explicit phylogenetic networks in peer-reviewed journals and their incorporation in a future database of published phylogenetic networks.Keywords
This publication has 15 references indexed in Scilit:
- PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationshipsBMC Bioinformatics, 2008
- A perl package and an alignment tool for phylogenetic networksBMC Bioinformatics, 2008
- Drawing explicit phylogenetic networks and their integration into SplitsTreeBMC Evolutionary Biology, 2008
- Dendroscope: An interactive viewer for large phylogenetic treesBMC Bioinformatics, 2007
- TBMap: a taxonomic perspective on the phylogenetic database TreeBASEBMC Bioinformatics, 2007
- Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)OMICS: A Journal of Integrative Biology, 2006
- A Special Issue on Data StandardsOMICS: A Journal of Integrative Biology, 2006
- Application of Phylogenetic Networks in Evolutionary StudiesMolecular Biology and Evolution, 2005
- Charting the Evolutionary History of LifeScience, 2003
- The Roots of PhylogenyScience, 1996