PhyloTempo: A Set of R Scripts for Assessing and Visualizing Temporal Clustering in Genealogies Inferred from Serially Sampled Viral Sequences.
PhyloTempo: A Set of R Scripts for Assessing and Visualizing Temporal Clustering in Genealogies Inferred from Serially Sampled Viral Sequences.
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DOI：
10.4137/ebo.s9738
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发表时间：
2012
期刊：
影响因子：
--
通讯作者：
Salemi M
中科院分区：
文献类型：
--
作者：
Norström MM;Prosperi MC;Gray RR;Karlsson AC;Salemi M
序列采样的核苷酸序列可以用来推断进化的病毒种群的人口学历史。系统发育树的形状往往反映了进化和生态过程之间的相互作用。有几种方法可以通过树的平衡、分枝模式和比较特性来分析系统发育树的拓扑和特征。时间聚类(TC)统计量是一种基于祖先特征重构的新的拓扑度量，它表征了系统发育的时间结构。在这里，PhyloTempo是第一个用R语言实现的TC，它在一个用户友好的图形框架中集成了其他几个拓扑度量。TC统计数据与其他指标的比较提供了对形成致病病毒进化的动态过程的多方面洞察。在连续采集的宿主内人类和猿类免疫缺陷病毒种群数据集上测试了PhyloTempo的特征和适用性。PhyloTempo是在GNU通用公共许可证下分发的，网址为https://sourceforge.net/projects/phylotempo/.
Serially-sampled nucleotide sequences can be used to infer demographic history of evolving viral populations. The shape of a phylogenetic tree often reflects the interplay between evolutionary and ecological processes. Several approaches exist to analyze the topology and traits of a phylogenetic tree, by means of tree balance, branching patterns and comparative properties. The temporal clustering (TC) statistic is a new topological measure, based on ancestral character reconstruction, which characterizes the temporal structure of a phylogeny. Here, PhyloTempo is the first implementation of the TC in the R language, integrating several other topological measures in a user-friendly graphical framework. The comparison of the TC statistic with other measures provides multifaceted insights on the dynamic processes shaping the evolution of pathogenic viruses. The features and applicability of PhyloTempo were tested on serially-sampled intra-host human and simian immunodeficiency virus population data sets. PhyloTempo is distributed under the GNU general public license at https://sourceforge.net/projects/phylotempo/.