What question did this study set out to answer?

To develop a maximum likelihood phylogenetic framework that accurately infers positive Darwinian selection in coding sequences despite the confounding presence of genetic recombination.

August 7, 2006BioinformaticsOpen Access

Robust inference of positive selection from recombining coding sequences

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To develop a maximum likelihood phylogenetic framework that accurately infers positive Darwinian selection in coding sequences despite the confounding presence of genetic recombination.
Developed a maximum likelihood method that permits phylogenetic tree topologies and branch lengths to vary across identified recombination breakpoints while modeling across-site synonymous rate variation.
Evaluated model performance using synthetic sequence simulations under extreme recombination scenarios and validated the method on empirical HIV-1 env and gag gene datasets.
Decreased false positive rates from >90% under standard phylogenetic methods down to acceptable levels in simulation tests while retaining high statistical power.
Detected significant positive selection in the empirical HIV-1 env gene dataset, but resolved previous false-positive signals in the HIV-1 gag gene, finding no significant evidence of selection.

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Implication

Simulation study demonstrates robust detection of positive selection in recombining viral sequences, indicating reduced false positive rates without sacrificing statistical power.

Cite This Study

Scheffler et al. (2006) studied this question.

synapsesocial.com/papers/6a951e3095cf49f4209e6ec6 https://doi.org/10.1093/bioinformatics/btl427

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Implication

Simulation study demonstrates robust detection of positive selection in recombining viral sequences, indicating reduced false positive rates without sacrificing statistical power.

Robust inference of positive selection from recombining coding sequences

Key Points

Discussion

Implication

Cite This Study

Robust inference of positive selection from recombining coding sequences

Key Points

Discussion

Implication

Cite This Study

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