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

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 netwo...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Gabriel Cardona, Francesc Rosselló, Gabriel Valiente
• Keywords: BMCBI 2008, Explicit Phylogenetic Networks, Molecular Phylogenetic Analysis, Phylogenetic Networks