NeEstimator v2: re‐implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. (31st August 2013)

• Record Type: Journal Article
• Authors: Do, C.; Waples, R. S.; Peel, D.; Macbeth, G. M.; Tillett, B. J.; Ovenden, J. R.
• Is Part Of: Molecular ecology resources. Volume 14:Number 1(2014:Jan.)
• Page Start: 209
• Page End: 214
• Publication Date: 2013-08-31
• Subjects: Molecular ecology -- Periodicals; 572.8
• DOI: 10.1111/1755-0998.12157
• Languages: English
• ISSNs: 1755-098X

Abstract

<abstract abstract-type="main" id="men12157-abs-0001"> <title>Abstract</title> <p> <sc>NeEstimator</sc> 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. <sc>NeEstimator</sc> 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.</p> </abstract>