Molecular Clocks

We have refned the relaxed clock models   to allow more than one branch to have the same rate value to remove   anticorrelation. In practice, this will only have any appreciable impact on   trees that have a small number of branches (<15 taxa). An effcient   implementation of the relaxed clock models that facilitates calculation of   Bayes Factors for model selection and model averaging of several clock models   has also be developed (Li and Drummond, 2012). Further, we provide a new   random local clock (RLC) model (Drummond and Suchard 2010), in which all   possible local clock confgurations and a strict clock are nested, providing a   convenient model to test for a strict clock. Heled and Drummond (2011) begins   to investigate alternative approaches to the calibration of tree priors with   fossil and geological evidence, and this area of research is still in its infancy.   Often, uncertainty exists in the age of viral RNA/DNA or ancient DNA samples   and these can now be incorporated (Shapiro et al. 2011), along with models   for sequence damage and error (Rambaut et al. 2009).  

分子钟

我们重新定义了松散的时钟模型，以允许多个分支具有相同的速率值来消除反相关。在实践中，这只会对枝条数量很少（<15个分类群）的树产生明显的影响。此外，还开发了实施有效的简化时钟模型，该模型有助于计算模型选择的贝叶斯因子和几个时钟模型的模型平均（Li and Drummond, 2012）。此外，我们还提供了一个新的随机局部时钟（RLC）模型（Drummond and Suchard 2010），其中嵌套了所有可能的局部时钟配置和严格的时钟，为测试严格的时钟提供了一个方便的模型。Heled和Drummond（2011）开始研究用化石和地质证据来校准树先验值，这一研究领域仍处于起步阶段。通常，病毒RNA/DNA或古代DNA样本的年龄存在不确定性，现在可以整合（Shapiro et al. 2011）到序列损伤和误差模型（Rambaut   et al. 2009）。