A Simple and Robust Statistical Test for Detecting the Presence of Recombination

By T. C. Bruen, Hervé Philippe, David Bryant. Genetics, 2006

1,325 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/54bf902c8947b012f01aab3839ae3a9d3b1dd002

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In Genetics

Citations in the corpus

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins (2014, methodology): “Using the tests for the presence of recombination implemented in PhiPack (54), it was found that both the spatial distribution of polymorphic sites (maximum χ2 test P-value of 0.”
An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets (2007, methodology): “Consider the tree in Figure 4.”
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes (2014, methodology): “Bases likely to have undergone recent recombination are identified using PhiPack [87].”
The early spread and epidemic ignition of HIV-1 in human populations (2014, background): “Table S8 lists the number of recombination events estimated as well as the difference between the expected φ-statistic under the assumption of no recombination and the observed φstatistic for the data sets generated using the different recombination rates (94).”
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic (2020, background): “%) incompatible splits in Neighbor-Nets (Bryant and Moulton, 2004), and (iii) a near-complete reduction of mosaic signal as identified by 3SEQ.”
Phylogeny and comparative phylogeography of Sclerurus (Aves: Furnariidae) reveal constant and cryptic diversification in an old radiation of rain forest understorey specialists (2013, methodology): “To evaluate the existence of significant evidence of recombination in Fib7, the pairwise homoplasy index (PHI) test (Bruen et al., 2006) was performed for each lineage using SplitsTree 4.”
Methicillin-Resistant Staphylococcus aureus: Molecular Characterization, Evolution, and Epidemiology (2018, background): “Recombination, for example, could increase the pathogenicity of a bacterium or increase its ability to disseminate, by diffusing genetic material throughout the rest of the bacterial population (384).”
Glacial expansion and diversification of an East Asian montane bird, the green‐backed tit (Parus monticolus) (2013, methodology): “For each nDNA locus, we tested for recombination using the Φw-statistic (Bruen et al., 2006) implemented in SplitsTree 4 (Huson & Bryant, 2006).”