Statistical Applications in Genetics and Molecular Biology
Editor-in-Chief: Stumpf, Michael P.H.
IMPACT FACTOR increased in 2015: 1.265
5-year IMPACT FACTOR: 1.423
Rank 42 out of 123 in category Statistics & Probability in the 2015 Thomson Reuters Journal Citation Report/Science Edition
SCImago Journal Rank (SJR) 2015: 0.954
Source Normalized Impact per Paper (SNIP) 2015: 0.554
Impact per Publication (IPP) 2015: 1.061
Mathematical Citation Quotient (MCQ) 2014: 0.17
Stopping-Time Resampling and Population Genetic Inference under Coalescent Models
1University of California, Berkeley
Citation Information: Statistical Applications in Genetics and Molecular Biology. Volume 11, Issue 1, Pages 1–20, ISSN (Online) 1544-6115, DOI: 10.2202/1544-6115.1770, January 2012
- Published Online:
To extract full information from samples of DNA sequence data, it is necessary to use sophisticated model-based techniques such as importance sampling under the coalescent. However, these are limited in the size of datasets they can handle efficiently. Chen and Liu (2000) introduced the idea of stopping-time resampling and showed that it can dramatically improve the efficiency of importance sampling methods under a finite-alleles coalescent model. In this paper, a new framework is developed for designing stopping-time resampling schemes under more general models. It is implemented on data both from infinite sites and stepwise models of mutation, and extended to incorporate crossover recombination. A simulation study shows that this new framework offers a substantial improvement in the accuracy of likelihood estimation over a range of parameters, while a direct application of the scheme of Chen and Liu (2000) can actually diminish the estimate. The method imposes no additional computational burden and is robust to the choice of parameters.