Data from: FlatNJ: a novel network-based approach to visualize evolutionary and biogeographical relationships

Split networks are a type of phylogenetic network that allow visualization of conflict in evolutionary data. We present a new method for constructing such networks called FlatNetJoining (FlatNJ). A key feature of FlatNJ is that it produces networks that can be drawn in the plane in which labels may appear inside of the network. For complex data sets that involve, for example, non-neutral molecular markers, this can allow additional detail to be visualized as compared to previous methods such as split decomposition and NeighborNet. We illustrate the application of FlatNJ by applying it to whole HIV genome sequences, where recombination has taken place, fluorescent proteins in corals, where ancestral sequences are present, and mitochondrial DNA sequences from gall wasps, where biogeographical relationships are of interest. We find that the networks generated by FlatNJ can facilitate the study of genetic variation in the underlying molecular sequence data and, in particular, may help to investigate processes such as intra-locus recombination. FlatNJ has been implemented in Java and is freely available at www.uea.ac.uk/computing/software/flatnj.

分裂网络（Split networks）是一类系统发育网络（phylogenetic network），可用于可视化演化数据中的冲突信号。本文提出一种构建此类网络的新方法，命名为FlatNetJoining（FlatNJ）。FlatNJ的核心特性在于，其生成的网络可在平面中绘制，且标签可置于网络内部。相较于分裂分解（split decomposition）与NeighborNet等传统方法，针对包含非中性分子标记的复杂数据集，该方法可呈现更多可视化细节。我们通过三类数据集展示FlatNJ的应用效果：一是发生重组的完整HIV基因组序列；二是带有祖先序列的珊瑚荧光蛋白序列；三是具有生物地理学关系研究价值的瘿蜂线粒体DNA序列。研究结果显示，FlatNJ生成的网络可助力底层分子序列数据的遗传变异研究，尤其有助于剖析基因座内重组等演化过程。FlatNJ已通过Java语言实现，并可在www.uea.ac.uk/computing/software/flatnj免费获取。