论文标题
在最大似然框架中产生过时的系统发育的经验指南
An empirical guide for producing a dated phylogeny with treePL in a maximum likelihood framework
论文作者
论文摘要
Treepl使用惩罚的似然方法在最大似然框架中产生过时的系统发育。自2012年出版以来，很少有资源来解释如何正确使用它。在本指南中，根据我的经验，我提供了一种使用Treepl产生过时的系统发育的逐步协议，该方案是基于我的经验，并构建了具有大量过时的系统发育，并对较小的系统发育进行了其他测试。我还提供了必要的数据，以重现介绍的示例系统发育之一。我将这些Treepl系统发育与Beast2建造的同行进行比较。即使我无法确切地解释Treepl的工作原理，但本指南中讨论的证据表明，提出的经验方案是可靠的。
treePL uses a penalised likelihood approach to produce a dated phylogeny in a maximum likelihood framework. Since its publication in 2012, few resources have been developed to explain how to use it properly. In this guide, I provide a step-by-step protocol for producing a dated phylogeny using treePL, based on my experience building a large dated phylogeny with it and conducting additional tests on a smaller phylogeny. I also provide the necessary data to reproduce one of the example phylogenies presented. I compare these treePL phylogenies to BEAST2-built counterparts. Even though I cannot explain precisely how treePL works, the evidence discussed in this guide suggest that the empirical protocol presented is reliable.
