A coalescent-based method for detecting and estimating recombination from gene sequences.

By G. McVean, P. Awadalla, Paul Fearnhead. Genetics, 2002

694 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/f360b56a76a7f9aa3e1e8c8274543923719b8167

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Citations in the corpus

The causes and consequences of HIV evolution (2004, background): “However, recent population-genetic studies indicate that recombination is also a pervasive force within subtype”
The evolution of molecular markers — just a matter of fashion? (2004, background): “However, it should be noted that several methods for estimating population parameters, such as migration and recombination, that take multiple hits into accoun”
Sex and virulence in Escherichia coli: an evolutionary perspective (2006, methodology): “Population-based recombination and mutation rates were estimated by a composite-likelihood method using LDHAT (McVean et al., 2002).”
A note on pseudolikelihood constructed from marginal densities (2004, background): “Fearnhead (2003) shows that the estimator of ρ based on a truncated version of 2 (ρ) is consistent as q → ∞ but that an approximation to 2 (ρ) used in McVean et al. (2002) does not give consistent estimation of ρ.”
Search for nucleotide diversity patterns of local adaptation in dehydrins and other cold-related candidate genes in Scots pine (Pinus sylvestris L.) (2008, methodology): “Estimates of population recombination rates per base pair for the set of seven loci were obtained also using the composite likelihood method of Hudson (2001) as implemented in LDhat2 software (McVean et al. 2002).”
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. (2003, background): “McVean et al. (2002) LRT is still accurate.”
Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths (2009, methodology): “We analyzed each core gene with LDHat, a coalescent-based estimator of recombination [38], and estimated an average ratio of recombination to mutation close to 1.”
RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets (2020, methodology): “Specifically, RDP5 uses the PHI test (Bruen, Philippe, and Bryan 2006) and 4-gamete test (McVean, Awadalla, and Fearnhead 2002) adapted versions of the homoplasy test (Maynard Smith and Smith 1998) to flag apparent recombination signals that are potentially attributable to a combination of…”
A Simple and Robust Statistical Test for Detecting the Presence of Recombination (2006, methodology): “Correlation of linkage disequilibrium with distance using r2 has been found to be the strongest nonparametric approach for detecting recombination within populations (McVean et al. 2002).”