While the majority have no issues, a few people are having trouble downloading software. We think that occasionally the server has exceptionally slow download speeds. This leads to get empty folders or software that doesn't execute. If this happens, try downloading at another time. If that doesn't work, use the Contact Us page and I can send you a dropbox link instead. Best, Jenny Ovenden
Download 32-bit and 64-bit versions for Mac, Linux and PC.
Now available in 64-bit for Mac and Linux platforms. A PC version will be available in due course. The 34-bit versions for all platforms are still available for download.
Minor Update of v2.1 March 2018 The update corrects an error in the mac version of the software where the output file had only headers (no content) when the Frequency Output file was chosen on the interface. Please download the latest version.
NeEstimator V2 is a tool for estimating contemporary effective population size (Ne) using multi-locus diploid genotypes from population samples. By ‘contemporary’ we mean that the estimates apply to the time period(s) encompassed by the samples (ie. individuals sampled and genotyped). Version 2.1 is a major update on V2.01. The changes largely enhance the linkage disequilibrium (LD) capacity of the software for the estimation of genetic effective population size. Enhancements include faster estimation of Burrows r, option to estimate r between loci on different chromosomes or linkage groups (user needs to upload linkage information), improved method of estimating jackknifed confidence intervals and improvements to handling low frequency alleles. Download the new version here.
The NeEstimator software development team has released a minor update to version 2.01. There was a typo in the v2.01 code that caused the lower jacknife confidence interval to be printed as ‘infinite’ when the upper interval was infinite. This has been corrected. Another minor issue has been fixed also. Previously the software did not correctly print out information about monomorphic loci for temporal samples. This problem occurred when one population consisted of several samples and there were monomorphic loci present. This was not an issue for the single-sample methods (LD, Hets Excess and Molecular Coancestry) You can download the software here.
The development team of Chi Do, Robin Waples, David Peel, Bree Tillett and Jenny Ovenden have been working together since March 2010 to produce this major re-write of the original NeEstimator software. The re-write brings together three methods that produce estimates of effective size from a single population sample of genotypes. It also implements the two-sample (ie temporal) method. In addition, there is an improved method for dealing with missing data within genotypes, options for screening out rare alleles allowing the user to evaluate their effects, confidence intervals for all estimates and corrections for temporal sampling when individuals are not removed from the population (ie Plan I sampling). The software is able to analyse large datasets with large (10,000 or more) numbers of genetic markers and there are options for batch processing large numbers of datasets. When not in batch mode, the software is controlled by a user friendly interface and there are versions for the mac, linux and PC. Watch out for the publication of the program note in Molecular Ecology Resources. Do, C., Waples, R. S., Peel, D., Macbeth, G. M., Tillet, B. J. & Ovenden, J. R. (In press). NeEstimator V2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources. Click on this link to download NeEstimator v2.0 and your feedback is appreciated.