Estimating Maximum Likelihood Phylogenies with PhyML
Estimating Maximum Likelihood Phylogenies with PhyML
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DOI：
10.1007/978-1-59745-251-9_6
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发表时间：
2009-01-01
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影响因子：
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通讯作者：
Gascuel, Olivier
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文献类型：
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作者：
Guindon, Stephane;Delsuc, Frederic;Gascuel, Olivier
我们对生物序列的起源、功能和/或结构的理解在很大程度上取决于我们破译分子进化机制的能力。这些复杂的过程可以通过系统发育框架中同源序列的比较来描述。此外，系统发育推断为从实际序列分析中展示分子进化的主要特征提供了可靠的统计工具。本章主要讨论最大似然原理下的系统发育树估计。在这种概率准则下推断的系统发生通常是可靠的，重要的生物学假设可以通过不同模型的比较来检验。估计ML系统发育在计算上要求很高，对结果进行仔细检查是必要的。本章重点介绍PhyM L，这是一个实现最新ML系统发育方法和算法的软件。我们通过对一个真实数据集的分析来说明这个程序的优点和缺点。PhyML v3.0可从http://atgc_montpellier.fr/phyml/获得。
Our understanding of the origins, the functions and/or the structures of biological sequences strongly depends on our ability to decipher the mechanisms of molecular evolution. These complex processes can be described through the comparison of homologous sequences in a phylogenetic framework. Moreover, phylogenetic inference provides Sound statistical tools to exhibit the main features of molecular evolution from the analysis of actual sequences. This chapter focuses on phylogenetic tree estimation under the maximum likelihood (ML) principle. Phylogenies inferred under this probabilistic criterion arc usually reliable and important biological hypotheses can be tested through the comparison of different models. Estimating ML phylogenics is computationally demanding, and careful examination of the results is warranted. This chapter focuses on PhyM L, a software that implements recent ML phylogenetic methods and algorithms. We illustrate the strengths and pitfalls of this program through the analysis of a real data set. PhyML v3.0 is available from http://atgc_montpellier.fr/phyml/.