Neighbor-Net: An agglomerative method for the construction of phylogenetic networks
Neighbor-Net: An agglomerative method for the construction of phylogenetic networks
复制标题
DOI：
10.1093/molbev/msh018
复制
发表时间：
2004-02-01
影响因子：
10.7
通讯作者：
Moulton, V
中科院分区：
文献类型：
--
作者：
Bryant, D;Moulton, V
在Saitou和Nei的Neighbor-Join(NJ)算法的基础上，提出了一种基于距离的构建系统发育网络的方法--Neighbor-Net。Neighbor-Net提供了数据的快照，可以指导更详细的分析。与分裂分解不同，邻居网络具有很好的伸缩性，可以快速为数百个分类群生成详细和信息丰富的网络。我们通过重新分析三个已发表的数据集来说明该方法：110个高度重组的沙门氏菌多位点序列分型序列的集合，Vigilant等人发表的135个“非洲之夜”人类线粒体序列，以及12个原始伴侣蛋白序列的集合，这些序列证明了基因转换的强有力证据。Neighbor-Net作为SplitsTree4软件包的一部分提供。
We present Neighbor-Net, a distance based method for constructing phylogenetic networks that is based on the Neighbor-Joining (NJ) algorithm of Saitou and Nei. Neighbor-Net provides a snapshot of the data that can guide more detailed analysis. Unlike split decomposition, Neighbor-Net scales well and can quickly produce detailed and informative networks for several hundred taxa. We illustrate the method by reanalyzing three published data sets: a collection of 110 highly recombinant Salmonella multi-locus sequence typing sequences, the 135 "African Eve" human mitochondrial sequences published by Vigilant et al., and a collection of 12 Archeal chaperonin sequences demonstrating strong evidence for gene conversion. Neighbor-Net is available as part of the SplitsTree4 software package.