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Open Access Highly Accessed Correspondence

Extended Newick: it is time for a standard representation of phylogenetic networks

Gabriel Cardona1, Francesc Rosselló1 and Gabriel Valiente2*

Author Affiliations

1 Department of Mathematics and Computer Science, University of the Balearic Islands, E-07122 Palma de Mallorca, Spain

2 Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034 Barcelona, Spain

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BMC Bioinformatics 2008, 9:532  doi:10.1186/1471-2105-9-532

Published: 15 December 2008

Abstract

Background

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).

Results

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.

Conclusion

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.