The NeEstimator software estimates the effective population sizes (N_e) from allele frequency data.

Product information

The NeEstimator software estimates the effective population sizes (N_e) from allele frequency data. The user can estimate N_e using any of the three internal methods or three third-party programs. Genotypes from a sample of the population are used as input. The user provides this data in GENEPOP, ARLEQUIN, simple columns (e.g. saved as a tab delimited text file from Microsoft Excel) or counts format.

The three internal methods are as follows.

• A point estimation method using linkage/gametic disequilibrium, (Hill, 1981).
  Robin Waples has released more recent software for calculating the genetic effective population size using a bias-corrected linkage disequilibrium method (see Waples, R. S., and Do, C. 2008. LDNE: a program for estimating effective populate size from data on linkage disequilibrium. Molecular Ecology Resources 8, 753-756, and Waples, R. S. 2006. A bias correction for estimates of effective popluation size based on linage disequilibrium at unlinked gene loci. Conservation Genetics 7, 167-184).
• A point estimation method using heterozygote excess (Pudovkin, Zaykin and Hedgecock, 1996).
• A temporal method using moments-based F-statistics (Krimbas and Tsakas, 1971; Nei and Tajima, 1981; Pollock, 1983 or Waples, 1989).

Register now to download NeEstimator.

The three third-party programs that NeEstimator uses are:

• A temporal method using a Bayesian-based approach called TM3. For more information, see the software download page based at the School of Animal and Microbial Sciences, University of Reading.
• A temporal method using a maximum likelihood based approach called MCLEEPS.
• A temporal method using a pseudo likelihood approach called MLNE.

Please note: the preferred citation to the software package is:
Ovenden, J., Peel, D., Street, R., Courtney, A., Hoyle, S. et al. (2007). The genetic effective and adult census size of an Australian population of tiger prawns (Penaeus esculentus). Molecular Ecology 16, 127-138.

Minimum computing requirements

The minimum computing requirements for running NeEstimator are as follows.

• A PC with any of the Microsoft Windows operating system versions listed below installed. It is assumed that if you are able to run one of these operating systems, you have enough computing power to run the NeEstimator software.
  • 95, 98, or ME
  • 2000, NT (version 4.0 with service pack 3 or later) with access to an Administrator account
• Approximately 4MB free hard disk space (not including user data space requirements).
• Mouse or compatible pointing device.
• Certain options require Microsoft Excel 97, 2000 or 2002.

Version changes

This section contains information about bug fixes and updates made to the previous version to achieve this version. Please send any problems or feedback that you have to Jennifer.Ovenden@dpi.qld.gov.au.

• Version 1.3
  • Fixed moments based temporal method so that it gives correct Ne when samples are more than one generation apart (confidence intervals were correct).
  • Removed reporting of confidence intervals from the heterozygote excess method until further investigation of the literature can be done.
  • Fixed bug in the implementation of linkage/gametic disequilibrium method which didn't give correct Ne.
  • Re-worked the Arlequin data format so that it works with Arlequin version 2.000's documented data format.
  • Re-worked the GenePop data format so that it works with GenePop version 3.4's documented data format.
  • Corrected so that it is now reading the minimum and maximum generation's data and not the first and second. This was a problem when there were more than two samples loaded and the last sample had allele values not present in the other two. This has also corrected problems with the method specific result tables.
  • Corrected stage three implementation of MCLEEPS which was using the stage two step size.
  • Implemented haploid data feature of TM3 in NeEstimator.
  • Fixed disappearing R values on Linkage Disequilibrium table.
  • Fixed Notepad button on TM3 results table that didn't work when TM3 was in a different directory to NeEstimator.
  • Fixed the use of the New, Open and Run menu items when an Analysis was already present with results and plots. The results and plots of the old analysis used to stay but are now killed.
  • Added question asking if the user wants to continue (eg Exit, New or Open menu items) when there are portions of the analysis not saved and continuing will mean losing these.
  • New F-statistics output file for each locus when using the moments based temporal method.
  • "Save Data As" menu item on NeEstimator menu works for GenePop, Arlequin and simple column data formats.

  • Result charts can now be generated in Excel 2002 (XP) as well as Excel 2000 and Excel 97 ("View Excel" button on MCLEEPS, MLNE and TM3 results tables only).

• Version 1.2
  • Fixed bug in the linkage/gametic disequilibrium method.
  • Fixed bug when user has an analysis open and they open another one but cancel it at the common dialog box. Previously that left the original with serious problems.
  • Added creation of "MCLEEPScon" batch file into NeEstimator so that this file is created just before MCLEEPS is run with the right input file name and in the same directory as "MCLEEPS.exe". This fixes the problem in the previous version that the patch was designed to fix.
  • Fixed bug where general results dialog would still appear even though no results were generated (usually due to an error).
  • Reduced size of help file considerably by using bitmaps with only 256 colours.
  • Added MLNE settings tab to analysis window
  • Updated help to include MLNE settings tab on analysis window.
  • Added count input data format (possibility of haploid data input for this format).
  • Updated help to include this new input data format.
  • Added file version number to analysis setting files. This version should still read older version's files but older versions of NeEstimator wont be able to read this version's files.
  • Added trouble shooting chapter to help file.
  • Added test data files to the installation file "NeEstimatorSetup.exe" and the topic "Running the Test Analysis" to the help file.
  • The "Details for Selected File" section on the Data Files tab of the Analysis dialog window now displays the full file name (including drive and path).

  • This version works with MLNE version 2.2 (which has been released since last release of NeEstimator).

• Version 1.1 - patch a

  • Missing file from setup program caused file error when MCLEEPS method was run. Other methods are not affected by this bug.

• Version 1.1
  • Added information on how to use the configure button/menu to online help.
  • Updated method information in online help.
  • Fixed inconsistencies with the way the program referred to the third party MLNE method.
  • Fixed problem with browse button on configure dialog. It used to only work once and then freeze.
  • Fixed problem with results from previous runs being present when a method was not run this time.
  • Updated to work with new version of MLNE (version 1.0).
  • Fixed problem with opening an ARLEQUIN formatted data analysis and the "Data Format" tab indicating incorrectly that the data is in GENEPOP format.
  • Reworked y-axis labelling in result plots.

  • Updated results printing (File-Print Results) to include MLNE results.

• Version 1.0
  • Major update of the user interface
  • Added third party method MLNE.
  • Added ability to plot likelihood curve for three third party methods.

Frequently asked questions

Please send any questions or feedback that you have to Jennifer.Ovenden@dpi.qld.gov.au.

Q: Is there a version of NeEstimator available for Macs?
A: No.

Q: How do I get a copy of NeEstimator?
A: Click on the link below to register yourself as a user of NeEstimator (enter your details in the spaces provided and click the submit button).  Download the NeEstimator installation file (neestimatorsetup.exe).

Q: How do I get NeEstimator started once I have downloaded the installation file?
A: Once you have a copy of the installation file on your computer, double-click this file's icon.  The installation wizard will open and lead you through the installation process.  Once the installation process is complete, you will be able to start the program (double-click on the file "NeEstimator.exe") and use the online help to guide you further.

Q: Can I use my data that is saved in Microsoft Access or Excel?
A: Yes you can use data from any program as long as you can save or export the data as a text file first (tab, space or comma delimited are all acceptable) and the data is in one of the accepted formats (GENEPOP, ARLEQUIN, simple columns or counts).  See the NeEstimator online help for more information about these accepted formats.

Q: Can I use NeEstimator with haploid data?
A: Yes, the counts input data format accepts counts of alleles per locus, and can be used to input allele frequencies for haploid loci.  The moments-based temporal method that is implemented in NeEstimator can be used to estimate female effective population size from mitochondrial DNA haplotype frequencies.

Q: What does "infinity" in the results mean?
A: This corresponds to the case where the method cannot distinguish a large N_e from infinity.  How large the true N_e has to be before this occurs depends on the method's power.  The power depends on several things including sample size, number of loci/alleles etc.  For each of the third party programs an upper limit for N_e is specified (see each program's documentation).  If this value is obtained, all that can be said is that the estimate is greater than this limit.

Q: How do I uninstall NeEstimator?
A: There is an uninstall program provided with NeEstimator.  There are several ways of activating this program (e.g. through the Add/Remove Programs in the Control Panel of Windows 2000) of which one is described here.  Find the file "uninstall.exe" in the NeEstimator installation directory (eg. "C:\Program Files\NeEstimator") and double-click it.  A message will ask "Are you sure you want to uninstall NeEstimator?", click "Yes".  NeEstimator will be uninstalled.  If the "Uninstalling NeEstimator" window asks, the two files "NeEstimator.adf" and "NeEstimator.GID" can be deleted.

References

Anderson E, Williamson E (2000). MCLEEPS software.

Beaumont MA (2002). TM3 software.  For more information about TM3, visit Mark Beaumont's software web page.

Hill WG (1981).  Estimation of effective population size from data on linkage disequilibrium.  Genetical Research 38, 209-216.

Krimbas CB, Tsakas S (1971).  The genetics of Dacus oleae.  V. Changes of esterase polymorphism in a natural population following insecticide contro: Selection of drift?   Evolution 15, 264-276.

Nei M, Tajima F (1981).  Genetic drift and estimation of effective population size.  Genetics 98, 625-640.

Pollock E (1983).  A new method for estimating the effective population size from allele frequency changes.  Genetics 104, 531-548.

Pudovkin AI, Zaykin DV, Hedgecock D (1996).  On the potential for estimating the effective number of breeders from heterozygote excess in progeny.  Genetics 144, 383-387.

Wang, J (2003).  MLNE software.

Waples RS (1989).  A generalized approach for estimating effective population size from temporal changes in allele frequency.  Genetics 121, 379-391.