Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.
By Maria Anisimova, Rasmus Nielsen, Ziheng Yang. Genetics, 2003
562 citations recorded by the source corpus.
View Paper: https://www.semanticscholar.org/paper/8d1fbe1b3934fed83ad381179defba5385c69698
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
- Ziheng Yang
- Edward C. Holmes
- Andrew Rambaut
- Keith A. Crandall
- Daniel J. Wilson
- Wendy S. W. Wong
- Yong‐Zhen Zhang
- Xavier Didelot
Citations in the corpus
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes (2015, methodology): “This effect is likely to contribute to the well-recognized distortion of branch lengths leading to spurious inference of demography, selection and molecular clocks when phylogenetic methods are applied to recombining populations [27,28,77,78].”
- The causes and consequences of HIV evolution (2004, background): “Moreover, recombination again complicates the analysis, as it might produce false-positive evidence for natural selection in measures of d N / d S”
- The Evolution and Emergence of RNA Viruses (2009, background): “In addition, although analysis of dN/dS provides a useful overview of the selection pressures that act on gene sequences, and which explains their popularity, it is also the case that attempts to use dN/dS to infer positive selection on individual amino acid sites or branches are inherently diffi cu”
- Molecular Evolution of Human Coronavirus Genomes (2016, unknown): “Thus, not only recombination is of interest per se, but failure to account for its presence can distort phylogeny-based analyses, including estimates of natural selection [66].”
- Bayes empirical bayes inference of amino acid sites under positive selection. (2005, background): “For example, simulations demonstrated that the LRTs are not robust to frequent intragenic recombinations (Anisimova, Nielsen, and Yang 2003).”
- PAML 4: phylogenetic analysis by maximum likelihood. (2007, background): “Anisimova et al. 2003; Wong et al. 2004) suggest that two pairs of site models are particularly”