The DOI matches its Crossref record; 16 of the 16 references it cites were found in a registry or an index.
MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus
Open accessAbstract
Motivation: We have implemented a coalescent simulation program for a structured population with selection at a single diploid locus. The program includes the functionality of the simulator ms to model population structure and demography, but adds a model for deme- and time-dependent selection using forward simulations. The program can be used, e.g. to study hard and soft selective sweeps in structured populations or the genetic footprint of local adaptation. The implementation is designed to be easily extendable and widely deployable. The interface and output format are compatible with ms. Performance is comparable even with selection included. Availability: The program is freely available from http://www.mabs.at/ewing/msms/ along with manuals and examples. The source is freely available under a GPL type license. Contact: gregory.ewing@univie.ac.at Supplementary information: Supplementary data are available at Bioinformatics online.
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Cites
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“Population structure, as well as demography and recombination, are readily incorporated into a coalescent framework (for review, Hein et al., 2005; Wakeley, 2008). To include selection into a simulator based on the coalescent, we extend the approach of Kaplan et al. (1989) and Barton et al.”
The “hitchhiking effect” revisited
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Kim, Y., & Stephan, W. (2002) · Genetics · doi:10.1093/genetics/160.2.765 · Cited by 631
Coalescent Theory: An Introduction
Wakeley, J. (2008) · Cited by 603
Coalescent Theory: An Introduction
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Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory
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ANGSD: Analysis of Next Generation Sequencing Data
Korneliussen, T. S., Albrechtsen, A., & Nielsen, R. (2014) · BMC Bioinformatics · doi:10.1186/s12859-014-0356-4 · Cited by 2,982
Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA
Huerta-Sánchez, E., Jin, X., Asan, Bianba, Z., Peter, B. M., Vinckenbosch, N., Liang, Y., Yi, X., He, M., Somel, M., et al. (2014) · Nature · doi:10.1038/nature13408 · Cited by 1,208
PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R
Pfeifer, B., Wittelsbürger, U., Ramos-Onsins, S. E., & Lercher, M. J. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu136 · Cited by 939
SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes
Pavlidis, P., Živković, D., Stamatakis, A., & Alachiotis, N. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst112 · Cited by 473
Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity
Andersen, E. C., Gerke, J. P., Shapiro, J. A., Crissman, J. R., Ghosh, R., Bloom, J. S., Félix, M.-A., & Kruglyak, L. (2012) · Nature Genetics · doi:10.1038/ng.1050 · Cited by 403
Metadata
- Authors
- Ewing, G., & Hermisson, J.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-06-30
- Volume
- 26
- Issue
- 16
- Pages
- 2064-2065
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2144658220
- Cited by
- 344
- References
- 16
- FWCI
- 9.72
- Type
- journal article
- Language
- en
- Open access
- hybrid
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