NeEstimator software

The NeEstimator software estimates genetic effective population sizes (Ne) from allele frequency data.

Price: This software is freely available for non-commercial scientific use
Download: DOWNLOAD – Please register your details before downloading this software. Note that the email addresses will only be used for notifying downloaders of new versions of the software.
Product author: NeEstimator development team
Release date: February 2014, updated in May 2014.
Version: 2.01
This version is a minor update of version 2.0
Download format: 1.5MB ZIP file

Product information

NeEstimator V2.01 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.

Four methods are available to calculate ; three single-sample (point estimation) methods and one two-sample (temporal) method.

NeEstimator V2.01 does not include third-party programs; all methods are implemented by NeEstimator V2 code.

The user needs to provide genotypic data in one of the accepted formats (FSTAT, GENEPOP).

The download package (a .zip folder) contains the graphical user interface (.jar), executables for PC, Mac or Linux, test input files, example output files, a help file (as .pdf and .html) and accessory files (mathematical details of methods implemented and files to facilitate batch processing of input files).

Preferred citation

When publishing results based on NeEstimator analyses, you should cite the original methods as well as NeEstimator program note. For example:

“We estimated Ne using the molecular co-ancestry method of Nomura (2008), as implemented in NeEstimator V2.01 (Do et al. In Press.).”

Do, C., Waples, R. S., Peel, D., Macbeth, G. M., Tillett, B. J. & 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, 209-214.

Computing requirements

NeEstimator V2.01 works on Windows, Linux and Mac operating systems. Java Runtime Environment (JRE) version 6 or above should be present on the user’s computer. Testing was performed on Windows XP, Windows Vista, and Windows 7, Linux Ubuntu 12.04 and Mac OS X 10.9. The software is expected to run on newer releases of these platforms.

Frequently asked questions

Q: Is there a version of NeEstimator V2 available for Mac or Linux?
A: Yes. The Java GUI is the same for all platforms; it calls a program called ‘Ne2L’ for Linux or ‘Ne2M’ for Mac computers. The user needs to download the correct program for their computer platform.

Q: How do I get a copy of NeEstimator V2?
A: Download the software from this web site using the link above.

Q: How do I get NeEstimator V2 started once I have downloaded the installation file?
A: Download the .zip package and expand it. Among other files, it contains the java executable files “NeGUI.jar”, the help file, the Ne-program for your system:

  • Ne2.exe or windows
  • Ne2M for Mac
  • Ne2L for Linux

The two files “NeGUI.jar” and the Ne-program should be in the same directory in your machine.

Once you have a copy of the installation file on your computer, double-click the icon for NeGUI.jar. You will now be able to use the software.

Q: Can I use my data that are saved in Microsoft Access or Excel?
A: Yes, you can use data from any program as long as it is saved as a text file in one of the accepted formats (GENEPOP, FSTAT).

Q: How do I uninstall NeEstimator?
Delete NeGUI.jar ,Ne2.exe, Ne2M or Ne2L for Windows, Mac or Linux respectively, the help file and empty the trash.

Q:  How will estimates from the LD method differ from previous implementations?

A:  The new implementation of the LD method includes the (Waples 2006) bias correction, which was not included in the version included in NeEstimator V1.3.  As a consequence, LD estimates from V2 will generally be lower than those from the previous implementation.  If there are no missing data, LD results from NeEstimator V2 should be identical to those obtained from LDNe (Waples & Do 2008).  Some differences can be expected if not all individuals have been scored for all loci, as V2 implements an improved method for dealing with missing data.

Q: How large a dataset can V2 accommodate?

A: The capacity for numbers of individuals, loci, and populations are very large, but we cannot at present identify a specific upper limit.  We have successfully run the LD method on a dataset with 20-30 individuals and >46,000 diallelic (SNP) loci using a 32-bit version of the software.  These analyses required consideration of over 1 billion pairwise comparisons of loci.  User feedback on experiences using large datasets would be appreciated.

Q: Is there a 64-bit version of the software?

A: A 64-bit version may be available in the future, if users request it.


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