%0 Journal Article %1 rasmussen2014genomewide %A Rasmussen, Matthew D. %A Hubisz, Melissa J. %A Gronau, Ilan %A Siepel, Adam %D 2014 %I Public Library of Science %J PLOS Genetics %K ARG along_the_genome methods %N 5 %P 1-27 %R 10.1371/journal.pgen.1004342 %T Genome-Wide Inference of Ancestral Recombination Graphs %U https://doi.org/10.1371/journal.pgen.1004342 %V 10 %X Author Summary The unusual and complex correlation structure of population samples of genetic sequences presents a fundamental statistical challenge that pervades nearly all areas of population genetics. Historical recombination events produce an intricate network of intertwined genealogies, which impedes demography inference, the detection of natural selection, association mapping, and other applications. It is possible to capture these complex relationships using a representation called the ancestral recombination graph (ARG), which provides a complete description of coalescence and recombination events in the history of the sample. However, previous methods for ARG inference have not been adequately fast and accurate for practical use with large-scale genomic sequence data. In this article, we introduce a new algorithm for ARG inference that has vastly improved scaling properties. Our algorithm is implemented in a computer program called ARGweaver, which is fast enough to be applied to sequences megabases in length. With the aid of a large computer cluster, ARGweaver can be used to sample full ARGs for entire mammalian genome sequences. We show that ARGweaver performs well in simulation experiments and demonstrate that it can be used to provide new insights about both demographic processes and natural selection when applied to real human genome sequence data.

@article{rasmussen2014genomewide, abstract = {Author Summary The unusual and complex correlation structure of population samples of genetic sequences presents a fundamental statistical challenge that pervades nearly all areas of population genetics. Historical recombination events produce an intricate network of intertwined genealogies, which impedes demography inference, the detection of natural selection, association mapping, and other applications. It is possible to capture these complex relationships using a representation called the ancestral recombination graph (ARG), which provides a complete description of coalescence and recombination events in the history of the sample. However, previous methods for ARG inference have not been adequately fast and accurate for practical use with large-scale genomic sequence data. In this article, we introduce a new algorithm for ARG inference that has vastly improved scaling properties. Our algorithm is implemented in a computer program called ARGweaver, which is fast enough to be applied to sequences megabases in length. With the aid of a large computer cluster, ARGweaver can be used to sample full ARGs for entire mammalian genome sequences. We show that ARGweaver performs well in simulation experiments and demonstrate that it can be used to provide new insights about both demographic processes and natural selection when applied to real human genome sequence data.}, added-at = {2020-06-30T00:59:10.000+0200}, author = {Rasmussen, Matthew D. and Hubisz, Melissa J. and Gronau, Ilan and Siepel, Adam}, biburl = {https://www.bibsonomy.org/bibtex/24cc258ada5b258e10633c4e60c09f3c7/peter.ralph}, doi = {10.1371/journal.pgen.1004342}, interhash = {3ee973237492c2f034fd6ec1af698097}, intrahash = {4cc258ada5b258e10633c4e60c09f3c7}, journal = {PLOS Genetics}, keywords = {ARG along_the_genome methods}, month = {05}, number = 5, pages = {1-27}, publisher = {Public Library of Science}, timestamp = {2020-06-30T00:59:10.000+0200}, title = {Genome-Wide Inference of Ancestral Recombination Graphs}, url = {https://doi.org/10.1371/journal.pgen.1004342}, volume = 10, year = 2014 }