Generalized neighbor-joining: More reliable phylogenetic tree reconstruction
Generalized neighbor-joining: More reliable phylogenetic tree reconstruction
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DOI：
10.1093/oxfordjournals.molbev.a026165
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发表时间：
1999-06-01
影响因子：
10.7
通讯作者：
Zhang, TT
中科院分区：
文献类型：
--
作者：
Pearson, WR;Robins, G;Zhang, TT
我们开发了一种系统发育树重建方法，可以检测和报告多个拓扑距离较远的低成本解决方案。我们的方法是对Saitou和Nei的邻居连接方法的推广，通过在其执行过程中跟踪多个部分解，提供了更彻底的解空间采样。解决方案空间采样的范围由一对用户指定的参数（备选解决方案的总数和随机选择的备选解决方案的数量）控制，从而在运行时间、解决方案质量和多样性之间实现平稳的权衡。该方法可以发现拓扑上不同的低成本解。在使用最小二乘距离或最小进化标准对生物和合成数据集进行测试时，该方法始终表现得与邻居连接启发式和Fitch-Margoliash距离度量的philips实现一样好，甚至更好。此外，该方法还可以识别出成本在最佳方案的1%或2%以内，但与最佳方案（16个分类群）的拓扑距离为9个或更多的替代树拓扑；对于32个分类群，当保留200个部分解时，从最佳拓扑中获得17个（最小二乘）和22个（最小进化）分区。因此，该方法可以剥离成本较低的树拓扑和与最佳拓扑有显著差异的近最佳树拓扑。
We have developed a phylogenetic tree reconstruction method that detects and reports multiple topologically distant low-cost solutions. Our method is a generalization of the neighbor-joining method of Saitou and Nei and affords a more thorough sampling of the solution space by keeping track of multiple partial solutions during its execution. The scope of the solution space sampling is controlled by a pair of user-specified parameters-the total number of alternate solutions and the number of alternate solutions that are randomly selected-effecting a smooth trade-off between run time and solution quality and diversity. This method can discover topologically distinct low-cost solutions. In tests on biological and synthetic data sets using either the least-squares distance or minimum-evolution criterion, the method consistently performed as well as, or better than, both the neighbor-joining heuristic and the PHYLIP implementation of the Fitch-Margoliash distance measure. In addition, the method identified alternative tree topologies with costs within 1% or 2% of the best, but with topological distances of 9 or more partitions from the best solution (16 taxa); with 32 taxa, topologies were obtained 17 (least-squares) and 22 (minimum-evolution) partitions from the best topology when 200 partial solutions were retained. Thus, the method can rind lower-cost tree topologies and near-best tree topologies that are significantly different from the best topology.