NeEstimator pipeline

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

 (5)
2018
PMCID: 5774298
PMID: 29362690
DOI: 10.7717/peerj.4173

[…] using the ld method (waples, 2006) updated for missing data and following peel et al. (2013). values of ne within corresponding 95% confidence intervals (ci) for each population were estimated using neestimator (do et al., 2014) 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 […]

2018
PMCID: 5913722
PMID: 29668011
DOI: 10.1590/1678-4685-GMB-2017-0052

[…] (rice, 1989)., two methods were used to estimate effective population size (n e), both assuming a closed population with discrete generations and random variance in reproductive success. the program neestimator v.2.01 (do et al., 2014) was used to estimate the parental generation n e from genotypic data based on the linkage disequilibrium (ld) method, which calculates separate estimates using […]

2016
PMCID: 5080595
PMID: 27782185
DOI: 10.1038/srep36095

[…] using nei’s genetic distance. the effective number of breeders (nb) was estimated for each yoy sample, using the linkage disequilibrium method23 with a 0.05 frequency cutoff, as implemented in neestimator24. ml-relate25 was used to estimate pairwise relatedness and heirfstat26 was used to estimate rarefied allelic richness. probability estimates based on multiple comparisons were corrected […]

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 [31]. a bias-corrected version of the ld method [32] was used to obtain the final estimate of ne., marker-based inbreeding coefficients for each breed were estimated using the gcta […]

2010
PMCID: 2876113
PMID: 20520795
DOI: 10.1371/journal.pntd.0000692

[…] to effective population size, a property exploited by the method from bartley et al. [40], which is in fact coming from hill [41] and modified by waples [42]. from equation 2 of [40], modified as in neestimator help file [43], allelic correlations (r) can be estimated as , where p and q are frequencies of allele a at locus 1 and allele b at locus 2, respectively and d is the so called (e.g. […]

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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