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ldne: a program for estimating effective population size from data on linkage disequilibrium
Abstract
ldne is a program with a Visual Basic interface that implements a recently developed bias correction for estimates of effective population size (N e) based on linkage disequilibrium data. The program reads genotypic data in standard formats and can accommodate an arbitrary number of samples, individuals, loci, and alleles, as well as two mating systems: random and lifetime monogamy. ldne calculates separate estimates using different criteria for excluding rare alleles, which facilitates evaluation of data for highly polymorphic markers such as microsatellites. The program also introduces a jackknife method for obtaining confidence intervals that appears to perform better than parametric methods currently in use.
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Cites
A leisurely look at the bootstrap, the jackknife, and cross-validation
Efron, B., & Gong, G. (1983) · The American Statistician · doi:10.1080/00031305.1983.10483087 · Cited by 3,229
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Navigating the temporal continuum of effective population size
Nadachowska‐Brzyska, K., Konczal, M., & Babik, W. (2022) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.13740 · Cited by 116
Zhang, W., Gao, X., Zhang, Y., Zhao, Y., Zhang, J., Jia, Y., Zhu, B., Xu, L., Zhang, L., Gao, H., et al. (2018) · BMC Genetics · doi:10.1186/s12863-018-0705-9 · Cited by 66
Sacks, B. N., Statham, M. J., Perrine, J. D., Wisely, S. M., & Aubry, K. B. (2010) · Conservation Genetics · doi:10.1007/s10592-010-0053-4 · Cited by 64
MOORE, J. A., TALLMON, D. A., NIELSEN, J., & PYARE, S. (2011) · Molecular Ecology · doi:10.1111/j.1365-294x.2011.05313.x · Cited by 46
Johnson, J. L., Wittgenstein, H., Mitchell, S. E., Hyma, K. E., Temnykh, S. V., Kharlamova, A. V., Gulevich, R. G., Vladimirova, A. V., Fong, H. W. F., Acland, G. M., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0127013 · Cited by 38
Unbiased estimation of linkage disequilibrium from unphased data
Ragsdale, A. P., & Gravel, S. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msz265 · Cited by 36
Gordicho, V., Vicente, J. L., Sousa, C. A., Caputo, B., Pombi, M., Dinis, J., Seixas, G., Palsson, K., Weetman, D., Rodrigues, A., et al. (2014) · Malaria Journal · doi:10.1186/1475-2875-13-423 · Cited by 29
Metadata
- Authors
- WAPLES, R. S., & DO, C.
- Venue
- Molecular Ecology Resources
- Publisher
- Wiley
- Published
- 2008-06-28
- Volume
- 8
- Issue
- 4
- Pages
- 753-756
- ISSN
- 1755-098X (ISSN-L)
- 1755-0998
- OpenAlex
- W2059051061
- Cited by
- 1,319
- References
- 1
- FWCI
- 28.48
- Type
- journal article
- Language
- en
- Open access
- closed
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