Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies
Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies
复制标题
DOI：
10.1093/bioinformatics/16.4.395
复制
发表时间：
2000-04-01
期刊：
影响因子：
5.8
通讯作者：
Rambaut, A
中科院分区：
文献类型：
--
作者：
Rambaut, A
动机：TipDate 是一个程序，它将使用在不同日期分离的序列来估计其分子进化速率。该程序提供了速率的最大似然估计以及序列最近共同祖先的相关敢于，在假设替换率（分子钟）恒定但适应隔离的模型下。还估计了这些参数的置信区间。结果：该方法应用于 17 种登革热病毒血清型 4 序列的样本，分离日期范围为 1956 年至 1994 年。该血清型的替换率估计为每年每个位点 7.91 x 10(-4) 替换（95% 置信区间为 6.07 x 10(-4) 9.86 x 10(-4))。这与这些序列最近的共同祖先的 1922 年日期（95% 置信区间为 1900-1936 年）兼容。
Motivation: TipDate is a program that will use sequences that have been isolated at different dates to estimate their rate of molecular evolution. The program provides a maximum likelihood estimate of the rate and also the associated dare of the most recent common ancestor of the sequences, under a model which assumes a constant rate of substitution (molecular clock) but which accommodates the elates of isolation. Confidence intervals for these parameters are also estimated.Results: The approach was applied to a sample of 17 dengue virus serotype 4 sequences, isolated at dates ranging from 1956 to 1994. The rate of substitution for this serotype was estimated to be 7.91 x 10(-4) substitutions per site per year (95% confidence intervals of 6.07 x 10(-4) 9.86 x 10(-4)). This is compatible with a date of 1922 (95% confidence intervals of 1900-1936) for the most recent common ancestor of these sequences.