Citations

GADMA citations

If you use GADMA in your research please cite:

[Noskova2020]Ekaterina Noskova, Vladimir Ulyantsev, Klaus-Peter Koepfli, Stephen J O’Brien, Pavel Dobrynin, GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data, GigaScience, Volume 9, Issue 3, March 2020, giaa005, https://doi.org/10.1093/gigascience/giaa005

If you use GADMA2 please cite:

[Noskova2023GADMA2]Ekaterina Noskova, Nikita Abramov, Stanislav Iliutkin, Anton Sidorin, Pavel Dobrynin, and Vladimir Ulyantsev, GADMA2: more efficient and flexible demographic inference from genetic data, GigaScience, Volume 12, August 2023, giad059, https://doi.org/10.1093/gigascience/giad059

If you use Bayesian optimization implemented GADMA please cite:

[Noskova2023BO]Ekaterina Noskova and Viacheslav Borovitskiy, Bayesian optimization for demographic inference, G3 Genes|Genomes|Genetics, Volume 13, Issue 7, July 2023, jkad080, https://doi.org/10.1093/g3journal/jkad080

Engine citations

If you use dadi as engine in GADMA please cite:

[Gutenkunst2009]RN Gutenkunst, RD Hernandez, SH Williamson, CD Bustamante “Inferring the joint demographic history of multiple populations from multidimensional SNP data” PLoS Genetics 5:e1000695 (2009).

If you use inbreeding inference with dadi engine in GADMA please cite:

[Blischak2020]Paul D Blischak, Michael S Barker, Ryan N Gutenkunst, Inferring the Demographic History of Inbred Species from Genome-Wide SNP Frequency Data, Molecular Biology and Evolution, Volume 37, Issue 7, July 2020, Pages 2124–2136, https://doi.org/10.1093/molbev/msaa042

If you use moments as engine in GADMA please cite:

[Jouganous2017]Jouganous, J., Long, W., Ragsdale, A. P., & Gravel, S. (2017). Inferring the joint demographic history of multiple populations: beyond the diffusion approximation. Genetics, 206(3), 1549-1567.

If you use moments.LD as engine in GADMA please cite:

[Ragsdale2019]Ragsdale, A. P., & Gravel, S. (2019) Models of archaic admixture and recent history from two-locus statistics. PLoS Genetics, 15(6), e1008204 (2019).
[Ragsdale2020]Ragsdale, A. P., & Gravel, S. (2020) Unbiased estimation of linkage disequilibrium from unphased data. Molecular Biology and Evolution 37.3 (2020): 923-932 (2020)

If you use momi as engine in GADMA please cite:

[Kamm2020]Kamm, J., Terhorst, J., Durbin, R., and Song, Y.S. Efficiently inferring the demographic history of many populations with allele count data. Journal of the American Statistical Association, Vol. 115, No. 531, (2020) 1472-1487.

CLAIC citation

If you evaluate CLAIC in GADMA please cite:

[Coffman2016]Alec J. Coffman, Ping Hsun Hsieh, Simon Gravel, Ryan N. Gutenkunst, Computationally Efficient Composite Likelihood Statistics for Demographic Inference, Molecular Biology and Evolution, Volume 33, Issue 2, February 2016, Pages 591–593, https://doi.org/10.1093/molbev/msv255