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@article{Ansari:2014:10.1534/genetics.113.157172,
author = {Ansari, MA and Didelot, X},
doi = {10.1534/genetics.113.157172},
journal = {Genetics},
title = {Inference of the Properties of the Recombination Process from Whole Bacterial Genomes.},
url = {http://dx.doi.org/10.1534/genetics.113.157172},
year = {2014}
}

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TY  - JOUR
AB  - Patterns of linkage disequilibrium, homoplasy and incompatibility are difficult to interpret because they depend on several factors, including the recombination process and the population structure. Here we introduce a novel model-based framework to infer recombination properties from such summary statistics in bacterial genomes. The underlying model is sequentially Markovian so that data can be simulated very efficiently, and we use approximate Bayesian computation techniques to infer parameters. As this does not require to calculate the likelihood function, the model can be easily extended to investigate less probed aspects of recombination. In particular, we extend our model to account for the bias in the recombination process whereby closely related bacteria recombine more often with one another. We show that this model provides a good fit to a dataset of Bacillus cereus genomes, and estimate several recombination properties, including the rate of bias in recombination. All the methods described in this paper are implemented in a software package which is freely available for download at http://code.google.com/p/clonalorigin/.
AU  - Ansari,MA
AU  - Didelot,X
DO  - 10.1534/genetics.113.157172
PY  - 2014///
TI  - Inference of the Properties of the Recombination Process from Whole Bacterial Genomes.
T2  - Genetics
UR  - http://dx.doi.org/10.1534/genetics.113.157172
UR  - http://www.ncbi.nlm.nih.gov/pubmed/24172133
ER  -

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