Relative Efficiencies of the Fitch-Margoliash, Maximum-Parsimony, Maximum-Likelihood, Minimum-Evolution, and Neighbor-joining Methods of Phylogenetic Tree Construction in Obtaining the Correct Tree
Relative Efficiencies of the Fitch-Margoliash, Maximum-Parsimony, Maximum-Likelihood, Minimum-Evolution, and Neighbor-joining Methods of Phylogenetic Tree Construction in Obtaining the Correct Tree
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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
DOI：
10.1093/oxfordjournals.molbev.a040572
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发表时间：
1989
影响因子：
10.7
通讯作者：
T. Imanishi
中科院分区：
文献类型：
--
作者：
N. Saitou;T. Imanishi
用计算机模拟的方法研究了几种造树方法获得正确的系统发育树的相对效率。所考察的方法是Fitch-Margoliash(FM)、最大简约(MP)、最大似然(ML)、最小进化(ME)和邻接法(NJ)。我们模拟了六个DNA序列的进化变化，每个序列的长度为300或600个核苷酸。考虑了核苷酸替换的恒定和变化速率。将所产生的DNA序列应用五种造树方法重建系统发育树，并与模式(正确)树进行比较。每例重复这一过程50次，得到以下结果：(1)FM方法获得正确树的效率明显低于其他方法。(2)NJ法和ME法在获得正确的树方面表现出较高的性能，它们的相对效率相似。(3)对于距离法(NJ、FM和ME)，当不同分支之间的替换率差异较大时，用修正的核苷酸替换得到的结果比用核苷酸差异得到的结果要好得多。(4)在假设核苷酸替换速率恒定的情况下，ML方法略逊于NJ和ME方法，但当分支间进化速度差异较大时，ML方法略好于后两种方法。如果考虑到所涉及的计算时间，NJ方法似乎是一种选择方法。
The relative efficiencies of several tree-making methods for obtaining the correct phylogenetic tree were studied by using computer simulation. The methods examined were the Fitch-Margoliash (FM), maximum-parsimony (MP), maximumlikelihood (ML), minimum-evolution (ME), and neighbor-joining (NJ) methods. We simulated the evolutionary changes of six DNA sequences each with a length of either 300 or 600 nucleotides. Both constant and varying rates of nucleotide substitution were considered. The DNA sequences generated were used to reconstruct phylogenetic trees by applying the five tree-making methods, and the trees obtained were compared with the model (correct) tree. This process was repeated 50 times for each case, and the following results were obtained: ( 1) The efficiency of obtaining the correct tree for the FM method was considerably lower than those for the other methods. (2) The NJ and ME methods showed a high performance in obtaining the correct tree, and their relative efficiencies were similar to each other. ( 3) For distance methods (NJ, FM, and ME), the results obtained by using corrected nucleotide substitutions were much better than those obtained by using nucleotide differences when the rate of substitution varied greatly among different branches. (4) The ML method was slightly inferior to the NJ and ME methods when a constant rate of nucleotide substitution was assumed, but it was slightly better than the latter two methods when the evolutionary rate varied drastically among branches. If one considers the computational time involved, the NJ method seems to be a method of choice.
系统发育树的重建和非恒定进化速率下分歧时间的估计。
DOI：
10.1101/sqb.1987.052.01.092
发表时间：
1987
期刊：
Cold Spring Harbor symposia on quantitative biology
影响因子：
--
作者：
Li,WH;Wolfe,KH;Sourdis,J;Sharp,PM
通讯作者：
Sharp,PM