Cardona Gabriel, Rosselló Francesc, Valiente Gabriel
Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca, Spain.
BMC Bioinformatics. 2008 Dec 15;9:532. doi: 10.1186/1471-2105-9-532.
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.
分子系统发育分析得出的系统发育树可从专业数据库以Newick格式获取，但对于系统发育网络而言，其能明确表示诸如重组、杂交或横向基因转移等网状进化事件，然而缺乏一种标准格式来表示它们阻碍了在专业文献中发表明确的系统发育网络以及将其纳入专业数据库。目前存在两种表示系统发育网络的不同提议：作为单个Newick字符串（其中每个杂交节点针对每个亲本都被拆分一次）或作为一组Newick字符串（每个杂交节点一个，再加上一个用于系统发育网络）。
我们倡导的作为扩展Newick格式的标准，将具有k个杂交节点的整个系统发育网络描述为带有k个重复节点的单个Newick字符串，并且一旦绘制出系统发育网络或确定子节点之间的顺序，这种表示就是唯一的。扩展Newick格式便于系统发育数据的共享和交换，还允许在计算机程序和脚本中实际使用系统发育网络。该标准最近已得到一些计算生物学家的认可，已经有几种系统发育工具支持它，并且避免了使用数量先验未知且无任何额外标记的Newick字符串来表示系统发育网络的各种缺点。
采用扩展Newick格式作为表示系统发育网络的标准，是朝着在同行评审期刊上发表明确的系统发育网络并将其纳入未来已发表系统发育网络数据库迈出的重要一步。
