ArticleEvolutionary bioinformatics online2012
PhyloTempo: A Set of R Scripts for Assessing and Visualizing Temporal Clustering in Genealogies Inferred from Serially Sampled Viral Sequences.
Article in Evolutionary bioinformatics online, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Limits of the Constant-rate Birth-Death Prior for Phylogenetic Tree Topology Inference.Systematic biology · 2024Pooled it
- Speciation completion rates have limited impact on macroevolutionary diversification.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Tree balance in phylogenetic models.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Phylogenetic meta-analysis of persistent SARS-CoV-2 infections in immunocompromised individuals highlights the challenges of robust evolutionary rate estimation caused by low genetic diversity.Virus evolution · 2025Article
- Inference of chromosome selection parameters and missegregation rate in cancer from DNA-sequencing data.Scientific reports · 2024Article
- Phylogenetic identification of influenza virus candidates for seasonal vaccines.Science advances · 2023Article
- Transmission cluster characteristics of global, regional, and lineage-specific SARS-CoV-2 phylogenies.IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine · 2022Article
- The evolutionary dynamics of endemic human coronaviruses.Virus evolution · 2021Article
- Network science inspires novel tree shape statistics.PloS one · 2021Article
- Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders.Zoological research · 2020Article
- Persistence of HIV transmission clusters among people who inject drugs.AIDS (London, England) · 2020Article
- Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders.Genome research · 2020Article
- Predicting the short-term success of human influenza virus variants with machine learning.Proceedings. Biological sciences · 2020Article
- Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study.PLoS computational biology · 2017Article
- Effects of memory on the shapes of simple outbreak trees.Scientific reports · 2016Article
- Phylogenetic tree shapes resolve disease transmission patterns.Evolution, medicine, and public health · 2014Article
- The intra-host evolutionary and population dynamics of human immunodeficiency virus type 1: a phylogenetic perspective.Infectious disease reports · 2013Review
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5 authors.
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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/.
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