Gu X, Zhang J
Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802.
Mol Biol Evol. 1997 Nov;14(11):1106-13. doi: 10.1093/oxfordjournals.molbev.a025720.
When the rate variation among sites is described by a gamma distribution, an important problem is how to estimate the shape parameter alpha, which is an index of the degree of among-site rate variation. The parsimony-based methods for estimating alpha are simple but biased, i.e., alpha tends to be overestimated. On the other hand, the likelihood-based methods are asymptotically unbiased but take a huge amount of computational time. In this paper, we have developed a new method to solve this problem: we first estimate the expected number of substitutions at each site, which is corrected for multiple hits, and then estimate the parameter alpha. Our method is computationally as fast as the parsimony method, and the estimation accuracy is much higher than that of parsimony and similar to that of the likelihood method.
当位点间的速率变化由伽马分布描述时，一个重要问题是如何估计形状参数α，它是位点间速率变化程度的一个指标。基于简约法估计α的方法简单但有偏差，即α往往被高估。另一方面，基于似然法的方法渐近无偏，但计算时间极长。在本文中，我们开发了一种新方法来解决这个问题：我们首先估计每个位点的预期替换数，并对多重击中进行校正，然后估计参数α。我们的方法在计算速度上与简约法一样快，估计精度比简约法高得多，与似然法相近。
