Charleston M A, Hendy M D, Penny D
Department of Mathematics, Massey University, Palmerston North, New Zealand.
J Comput Biol. 1994 Summer;1(2):133-51. doi: 10.1089/cmb.1994.1.133.
Simulations were used to study the performance of several character-based and distance-based phylogenetic methods in obtaining the correct tree from pseudo-randomly generated input data. The study included all the topologies of unrooted binary trees with from 4 to 10 pendant vertices (taxa) inclusive. The length of the character sequences used ranged from 10 to 10(5) characters exponentially. The methods studied include Closest Tree, Compatibility, Li's method, Maximum Parsimony, Neighbor-joining, Neighborliness, and UPGMA. We also provide a modification to Li's method (SimpLi) which is consistent with additive data. We give estimations of the sequence lengths required for given confidence in the output of these methods under the assumptions of molecular evolution used in this study. A notation for characterizing all tree topologies is described. We show that when the number of taxa, the maximum path length, and the minimum edge length are held constant, there it little but significant dependence of the performance of the methods on the tree topology. We show that those methods that are consistent with the model used perform similarly, whereas the inconsistent methods, UPGMA and Li's method, perform very poorly.
利用模拟研究了几种基于特征和基于距离的系统发育方法从伪随机生成的输入数据中获取正确树的性能。该研究涵盖了具有4至10个悬垂顶点（分类单元）的无根二叉树的所有拓扑结构（包括4个和10个）。所使用的字符序列长度呈指数分布，范围从10到10⁵个字符。所研究的方法包括最近树法、相容性法、李法、最大简约法、邻接法、相邻法和UPGMA法。我们还对李法进行了一种与加性数据一致的修改（简化李法）。在本研究中使用的分子进化假设下，我们给出了这些方法输出具有给定置信度所需序列长度的估计。描述了一种表征所有树拓扑结构的符号。我们表明，当分类单元数量、最大路径长度和最小边长度保持恒定时，这些方法的性能对树拓扑结构几乎没有但存在显著依赖性。我们表明，那些与所使用模型一致的方法表现相似，而不一致的方法，即UPGMA法和李法，表现非常差。
