系统发育中分支的统计检验

Full Reconstruction of Non-Stationary Strand-Symmetric Models on Rooted Phylogenies

Understanding the evolutionary relationship among species is of fundamental importance to the biological sciences. The location of the root in any phylogenetic tree is critical as it gives an order to evolutionary events. None of the popular models of nucleotide evolution used in likelihood or Bayesian methods are able to infer the location of the root without exogenous information. It is known that the most general Markov models of nucleotide substitution can also not identify the location of the root or be fitted to multiple sequence alignments with less than three sequences. We prove that t…

功能值性状的进化推断：系统发育的高斯过程回归

Evolutionary Inference for Function-valued Traits: Gaussian Process Regression on Phylogenies

生物学数据对象通常具有以下两个特征：（i）它们是函数而不是单个数字或向量，以及（ii）它们由于系统发育关系而相关。在本文中，我们给出了一个灵活的统计模型，这样的数据，通过结合假设从遗传学与高斯过程。我们描述了它作为一个非参数贝叶斯先验分布的使用，无论是预测（放置后验分布的祖先的功能）和模型选择（比较进化率跨越一个遗传，或确定最有可能的遗传与观察到的数据一致）。我们的工作是综合性的，将流行的系统发育布朗运动和Ornstein-Uhlenbeck模型扩展到功能数据和贝叶斯推断，并将高斯过程回归扩展到遗传学。我们提供了一个简单的说明我们的方法的应用。

Nested partitions from hierarchical clustering statistical validation

We develop a greedy algorithm that is fast and scalable in the detection of a nested partition extracted from a dendrogram obtained from hierarchical clustering of a multivariate series. Our algorithm provides a $p$-value for each clade observed in the hierarchical tree. The $p$-value is obtained by computing a number of bootstrap replicas of the dissimilarity matrix and by performing a statistical test on each difference between the dissimilarity associated with a given clade and the dissimilarity of the clade of its parent node. We prove the efficacy of our algorithm with a set of benchmarks…

分子传染病流行病学：生存分析与将系统发育树链接到传播树的算法

Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees

本文提出在生存分析框架下开发算法，利用系统发育树与流行病学数据的一一对应关系枚举传播树，从而更高效地估计传染性风险比和基线风险，为分子传染病流行病学提供严谨灵活的统计基础。