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Evol Bioinform Online. 2012;8:261-9. doi: 10.4137/EBO.S9738. Epub 2012 Jun 11.

PhyloTempo: A Set of R Scripts for Assessing and Visualizing Temporal Clustering in Genealogies Inferred from Serially Sampled Viral Sequences.

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  • 1Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden.

Abstract

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/.

KEYWORDS:

clustering; coalescence; comparative methods; fast evolving viruses; longitudinal samples; phylodynamics; phylogenetics; positive selection; software

PMID:
22745529
[PubMed]
PMCID:
PMC3382462
Free PMC Article
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