Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP*.
Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP*.
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DOI：
10.1080/10635150701281102
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发表时间：
2007-04
影响因子：
6.5
通讯作者：
T. H. Ogden;T. H. Ogden;Michael S. Rosenberg
中科院分区：
文献类型：
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作者：
T. H. Ogden;T. H. Ogden;Michael S. Rosenberg
最近开发了用于同时估计比对和系统发育的直接优化框架。在POY程序中实现的一种这样的方法在可变长度序列的分析(例如，使用核糖体基因的分析)和组合证据分析(形态+多基因)中变得越来越普遍。对包含插入和缺失事件的序列进行模拟，以便直接比较PAUP*中广泛使用的多序列比对方法(ClustanW)和随后的简约分析方法与通过POY进行的直接优化。在不同条件下(钟形、非钟形和超长)对梳状、平衡和随机树形状的数据集进行了模拟。计算并比较了POY的隐含比对和ClustaW的多序列比对的比对精度分数。在几乎所有的情况下(99.95%)，根据正确识别的同源位点的比例判断，CluastW产生的比对比POY隐含的比对更准确。还比较了POY拓扑和基于POUP*的简约生成的拓扑的拓扑精度(到真实树的距离)。在44.94%的病例中，通过PAUP*重建的Clustal比对树比POY更准确，而在16.71%的病例中，POY重建在拓扑上更准确(38.38%的时间与POY相同)。POY假设对齐与真实对齐的比较表明，平均而言，随着对齐误差的增加，拓扑精度降低。
Direct optimization frameworks for simultaneously estimating alignments and phylogenies have recently been developed. One such method, implemented in the program POY, is becoming more common for analyses of variable length sequences (e.g., analyses using ribosomal genes) and for combined evidence analyses (morphology + multiple genes). Simulation of sequences containing insertion and deletion events was performed in order to directly compare a widely used method of multiple sequence alignment (ClustalW) and subsequent parsimony analysis in PAUP* with direct optimization via POY. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (clocklike, non-clocklike, and ultrametric). Alignment accuracy scores for the implied alignments from POY and the multiple sequence alignments from ClustalW were calculated and compared. In almost all cases (99.95%), ClustalW produced more accurate alignments than POY-implied alignments, judged by the proportion of correctly identified homologous sites. Topological accuracy (distance to the true tree) for POY topologies and topologies generated under parsimony in PAUP* from the ClustalW alignments were also compared. In 44.94% of the cases, Clustal alignment tree reconstructions via PAUP* were more accurate than POY, whereas in 16.71% of the cases POY reconstructions were more topologically accurate (38.38% of the time they were equally accurate). Comparisons between POY hypothesized alignments and the true alignments indicated that, on average, as alignment error increased, topological accuracy decreased.