Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site.
Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site.
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当替代率随位点变化时，最大似然法、邻接法和最大简约法的相对效率。
DOI：
10.1093/oxfordjournals.molbev.a040108
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发表时间：
1994
影响因子：
10.7
通讯作者：
Nei,M
中科院分区：
文献类型：
--
作者：
Tateno,Y;Takezaki,N;Nei,M
在假设不同核苷酸位点之间的取代率存在变化或没有变化的情况下，通过计算机模拟研究了最大似然法（ML）、邻域连接法（NJ）和最大简约法（MP）在获得正确拓扑结构和估计四种DNA序列分支长度方面的相对效率。对于NJ方法，使用了几种不同的距离度量（Jukes-Cantor， Kimura双参数和gamma距离），而对于ML方法，使用了三种不同的转移/翻转比率(R)。MP方法采用标准不加权简约法和动态加权简约法。得到的结果如下：(1)当R值较大时，动态加权简约法比非加权简约法更能获得正确的拓扑。(2)然而，即使在MP方法给出一致树的情况下，加权和未加权的简约方法通常也不如NJ和ML方法有效。(3)当ML方法的所有假设都满足时，该方法的效率略高于NJ方法。然而，当假设不满足时，具有伽马距离的NJ方法在获得正确拓扑方面略优于ML方法。一般来说，这两种方法表现出或多或少相同的性能。NJ方法可以给出一个正确的拓扑，即使当使用的距离度量不是核苷酸取代的无偏估计。(4)对于ML和NJ方法，具有正确拓扑结构的树的分支长度估计比违反所使用的数学模型的假设更容易受到影响。在某些条件下，分支长度被严重高估或低估。MP方法通常会严重低估某些分支。(5)产生正确拓扑的距离度量，具有高概率，不一定能给出分支长度的良好估计。(6)在Felsenstein的DNAML中，用于检验分支长度估计的统计性的似然比检验和置信限检验对违反假设非常敏感，并且通常过于自由，无法用于实际数据。Rzhetsky和Nei的分支长度检验比Felsenstein的检验对假设的违反不那么敏感。(7)当序列发散度<或= 5%时，当使用>或= 1,000个核苷酸时，这三种方法在获得正确拓扑和估计分支长度方面的效率基本相同。（摘要删节为400字）
The relative efficiencies of the maximum-likelihood (ML), neighbor-joining (NJ), and maximum-parsimony (MP) methods in obtaining the correct topology and in estimating the branch lengths for the case of four DNA sequences were studied by computer simulation, under the assumption either that there is variation in substitution rate among different nucleotide sites or that there is no variation. For the NJ method, several different distance measures (Jukes-Cantor, Kimura two-parameter, and gamma distances) were used, whereas for the ML method three different transition/transversion ratios (R) were used. For the MP method, both the standard unweighted parsimony and the dynamically weighted parsimony methods were used. The results obtained are as follows: (1) When the R value is high, dynamically weighted parsimony is more efficient than unweighted parsimony in obtaining the correct topology. (2) However, both weighted and unweighted parsimony methods are generally less efficient than the NJ and ML methods even in the case where the MP method gives a consistent tree. (3) When all the assumptions of the ML method are satisfied, this method is slightly more efficient than the NJ method. However, when the assumptions are not satisfied, the NJ method with gamma distances is slightly better in obtaining the correct topology than is the ML method. In general, the two methods show more or less the same performance. The NJ method may give a correct topology even when the distance measures used are not unbiased estimators of nucleotide substitutions. (4) Branch length estimates of a tree with the correct topology are affected more easily than topology by violation of the assumptions of the mathematical model used, for both the ML and the NJ methods. Under certain conditions, branch lengths are seriously overestimated or underestimated. The MP method often gives serious underestimates for certain branches. (5) Distance measures that generate the correct topology, with high probability, do not necessarily give good estimates of branch lengths. (6) The likelihood-ratio test and the confidence-limit test, in Felsenstein's DNAML, for examining the statistical of branch length estimates are quite sensitive to violation of the assumptions and are generally too liberal to be used for actual data. Rzhetsky and Nei's branch length test is less sensitive to violation of the assumptions than is Felsenstein's test. (7) When the extent of sequence divergence is < or = 5% and when > or = 1,000 nucleotides are used, all three methods show essentially the same efficiency in obtaining the correct topology and in estimating branch lengths.(ABSTRACT TRUNCATED AT 400 WORDS)
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单个美洲印第安部落内存在广泛的线粒体多样性。
DOI：
10.1073/pnas.88.19.8720
发表时间：
1991
影响因子：
11.1
作者：
Ward,RH;Frazier,BL;Dew-Jager,K;Pääbo,S
通讯作者：
Pääbo,S
DOI：
10.1073/pnas.89.18.8741
发表时间：
1992-09-15
影响因子：
11.1
作者：
COOPER, A;MOURERCHAUVIRE, C;PAABO, S
通讯作者：
PAABO, S
影响因子：
10.7
作者：
B. Hedges;K. D. Moberg;Linda
通讯作者：
B. Hedges;K. D. Moberg;Linda
系统发育树构建的 Fitch-Margoliash、最大简约、最大似然、最小进化和邻接方法在获得正确树方面的相对效率
影响因子：
10.7
作者：
N. Saitou;T. Imanishi
通讯作者：
T. Imanishi
影响因子：
56.9
作者：
VIGILANT, L;STONEKING, M;WILSON, AC
通讯作者：
WILSON, AC