NeEstimator protocols

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NeEstimator specifications

Information


Unique identifier OMICS_19563
Name NeEstimator
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input format GENEPOP, FSTAT
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 2.01
Registration required Yes
Maintained Yes

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Maintainer


  • person_outline Jennifer Ovenden <>

Publication for NeEstimator

NeEstimator in pipelines

 (6)
2018
PMCID: 5774298
PMID: 29362690
DOI: 10.7717/peerj.4173

[…] of clusters were determined using the ld method () updated for missing data and following . values of ne within corresponding 95% confidence intervals (ci) for each population were estimated using neestimator () with the following parameters: a minimum allele frequency cutoff of 0.01 and a random mating model. in addition, we estimated a traditional calculation of ne for a stepwise mutation […]

2017
PMCID: 5737441
PMID: 29045601
DOI: 10.1093/gbe/evx215

[…] a data set that reasonably estimates the overall neutral genetic differentiation between populations. effective population sizes were estimated using the linkage disequilibrium method implemented in neestimator ()., we investigated the number of populations (or clusters) represented in our entire sampling using faststructure () and the putatively neutral snp data set, default parameters, […]

2016
PMCID: 4732815
PMID: 26824579
DOI: 10.1371/journal.pone.0147941

[…] were calculated for each breed using the same parameters mentioned previously., the effective population size (ne) was estimated using the linkage disequilibrium method implemented by the program neestimator version 2.01 []. to avoid bias from close linkage between loci, 10,000 evenly placed snps from across the genome were selected for inclusion in the ne calculation. the genome was divided […]

2016
PMCID: 4827816
PMID: 27064784
DOI: 10.1371/journal.pone.0153098

[…] [] using genetix 4.05.2 []. allelic richness (ar) was calculated using fstat v. 2.9.3.2 []. we estimated effective population sizes (ne) using the linkage disequilibrium method in program neestimator v.2.01 [], estimating 95% confidence intervals using jack knifing and excluding rare alleles with frequencies less than 0.02. it has been suggested that this approach, which is based […]

2015
PMCID: 4659207
PMID: 26602211
DOI: 10.1186/s12711-015-0169-6

[…] higher than 0.98 and if the lower bound was higher than 0.7., effective population size (ne) was calculated for each breed using the default parameters and the random mating model in the software neestimator v2 []. a bias-corrected version of the ld method [] was used to obtain the final estimate of ne., marker-based inbreeding coefficients for each breed were estimated using the gcta […]


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NeEstimator in publications

 (92)
PMCID: 5896141
PMID: 29642844
DOI: 10.1186/s12862-018-1171-8

[…] would be expected with founder effects or recent population bottlenecks []. contemporary ne was also calculated for each of the samples in both species according to the ld method implemented in neestimator v2.01 []., two independent mann-whitney u tests were conducted to test whether there were significant differences in the levels of mitochondrial (hr) and microsatellite (ar) diversities […]

PMCID: 5882862
PMID: 29615810
DOI: 10.1038/s41598-018-23587-w

[…] 1.31 under the assumption of a minimum allele frequency of 2% to minimise potential bias caused by rare alleles, (iii) the heterozygote excess method, and (iv) the molecular coanchestry method (neestimator v2.01)., in order to infer the population structure, we used the bayesian clustering algorithm as implemented in structure version 2.3.4 under the assumption of an admixture model […]

PMCID: 5838079
PMID: 29531691
DOI: 10.1002/ece3.3912

[…] using genepop version 4.5.1 (raymond & rousset, ; rousset, ). values of f is were computed using the method of weir and cockerham (), and exact p‐values were by the markov chain method., neestimator v2.01 is freely available software designed to estimate effective population size using three single‐sample methods and three‐two‐sample (moment‐based temporal) methods (do et al., ). […]

PMCID: 5774695
PMID: 29351326
DOI: 10.1371/journal.pone.0190799

[…] in these measures between pre- and post-supplementation samples were tested for significance with wilcoxon signed-rank tests. estimates of the effective number of breeders were made with the program neestimator [], making use of the linkage disequilibrium method []., a significant interaction between study period (before vs after) and category (supplemented vs non-supplemented) indicated […]

PMCID: 5817140
PMID: 29468027
DOI: 10.1002/ece3.3826

[…] frequencies for the adult and hatchling groups. the effective population size was calculated using adult individuals according to the linkage disequilibrium method of waples () as implemented in neestimator v. 2.01 (do et al., )., mlh was estimated according to three different approaches: standardized heterozygosity (sh; coltman, pilkington, smith, & pemberton, ), internal relatedness […]


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NeEstimator institution(s)
Conservation Biology Division, Northwest Fisheries Science Center, Seattle, WA, USA; NOAA Fisheries, Northwest Fisheries Science Centre, Seattle, WA, USA; CSIRO Mathematics and Informatics and Statistics. Castray Esplanade, Hobart, Tasmania, Australia; Queensland Government, Department of Agriculture, Fisheries and Forestry Brisbane, Queensland, Australia; Australian Institute of Marine Science, UWA Oceans Institute, Crawley, Western Australia, Australia; Molecular Fisheries Laboratory, School of Biomedical Sciences, University of Queensland, St Lucia, Queensland, Australia

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