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

Do, C., Waples, R. S., Peel, D., Macbeth, G. M., Tillett, B. J. and Ovenden, J. R. (2014) NeEstimator v2: Re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources, 14 1: 209-214. doi:10.1111/1755-0998.12157


Author Do, C.
Waples, R. S.
Peel, D.
Macbeth, G. M.
Tillett, B. J.
Ovenden, J. R.
Title NeEstimator v2: Re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data
Journal name Molecular Ecology Resources   Check publisher's open access policy
ISSN 1755-098X
1755-0998
Publication date 2014-01-01
Year available 2013
Sub-type Article (original research)
DOI 10.1111/1755-0998.12157
Open Access Status Not yet assessed
Volume 14
Issue 1
Start page 209
End page 214
Total pages 6
Place of publication Oxford, United Kingdom
Publisher Wiley-Blackwell
Language eng
Abstract 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.
Keyword Heterozygote-excess
Linkage disequilibrium
Molecular coancestry
Plan I and II temporal sampling
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Article first published online: 30 August 2013.

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2014 Collection
School of Biomedical Sciences Publications
 
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