NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne ) from genetic data

Mol Ecol Resour. 2014 Jan;14(1):209-14. doi: 10.1111/1755-0998.12157. Epub 2013 Aug 31.


NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single-sample estimators (updated versions of the linkage disequilibrium and heterozygote-excess methods, and a new method based on molecular coancestry), as well as the two-sample (moment-based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10 000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross-method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under MacOS, Linux and Windows.

Keywords: Plan I and II temporal sampling; heterozygote-excess; linkage disequilibrium; molecular coancestry.

MeSH terms

  • Computational Biology / methods*
  • Population Density*
  • Software*