Product information

NeOGen (genetic N_e for Overlapping Generations analysis; pronounced Neo-gen) is point-&-click genetic effective population size (N_e) and demographic modelling software. The software, initially designed for sharks, is applicable to many overlapping-generation species with moderate to low population sizes and fecundity (such as mammals). NeOGen provides a cohesive linkage disequilibrium genetic N_e estimate (N_e.LD) analysis and population simulation framework that simulates both the demography and genetic composition of a population, given a small subset of fundamental species-specific life-history, demographic and genetic priors.  NeOGen then guides the researchers in-silico to establish a tractable sampling regime, resulting in the numbers of samples and loci required to give accurate and precise N_e.LD estimates when empirical sampling is performed in the field.

Preferred citation

Blower D, Riginios C, Ovenden JR (2019) NeOGen: a tool to predict genetic effective population size (Ne) for low-fecundity species with generational overlap and to assist empirical Ne study design. Molecular Ecology Resources 19: 260-271 doi:10.1111/1755-0998.12941

License information

The Alpha and Beta versions of this software and documentation are currently Draft, Confidential, & Copyright Dean Blower 2018 All Rights Reserved.  This is to protect our intellectual property until the software is accepted for publication (currently in review with journal Molecular Ecology Resources). When accepted for publication the software will be free and open source. Future stable releases (i.e. not alpha or beta test versions) will be licensed with a GNU General Public License (GPL) license: https://opensource.org/licenses/GPL-3.0

Computing requirements

The minimum computing requirements for running NeOGen are as follows.

A PC is needed 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 NeOGen-Power software.

• Windows 7, 8, & 10, 64-bit (32-bit not available yet)
• Minimum 4GB RAM
• Microsoft Visual C++ 2008 Redistributable Package – This is typically already installed on many Windows machines. If it is already installed, the NeOGen Setup will attempt to install it.
• Approximately 1 GB free hard disk space (not including user data space requirements).
• Best viewed a screen resolution 1280×768 with text size of 100% (i.e. not enlarged).
• Mouse or compatible pointing device.
• User-specified PDF-viewer (eg. Adobe Acrobat or equivalent)

Further information

Installation details are described in the README file here.

The user manual can be downloaded here.

Four screen shots showing the software in operation are available; the Scenario specification screen, the Scenario results screen, the Sampling Strategy specification screen, and the Sampling Strategy results screen

For details on what’s new in the latest version, download the CHANGE-LOG file here.

Frequently asked questions

Q: Is there a version of NeOGen available for Linux and/or Macs?
A: No. Hopefully, we can supply a version compatible with your OS in the next versions.

Q: How do I get a copy of NeOGen?
A:  Click on the link below to open the NeOGen registration page. Register yourself as a user of NeOGen (enter your details in the spaces provided and click the submit button), then download the NeOGen installation file (Setup-NeOGen.exe).

Q: How do I get NeoGen started once I have downloaded the installation file?
A: Please use the following installation procedure:

1. Download the Setup EXE file.
2. Double-click the Setup EXE to start installation.
3. Specify the installation drive & folder. Using the default folder is recommended. Do NOT use a windows system reserved folder e.g. C:\Windows\Program Files, as security permissions may prevent correct NeOGen operation. Install to a permanently attached drive. Installing to a removable drive, e.g. USB drive, is not recommended.
4. Follow the prompts to finalise the installation. Use the default values for best results.
5. Double-click the NeOGen shortcut (on the desktop, in the start menu, or in the installation folder) to start NeOGen. Don’t start it with the NOGP.exe.
6. You’re done! Start exploring the wonder of NeOGen. Reading the guides will help ;o). The user manual (i.e. help file, guide 0) is displayed alongside the main app when its launched.

Q: How do I uninstall NeoGen?
A: Uninstall NeOGen from the Windows Programs & Features Control Panel screen by clicking on the NeOGen entry. Alternatively, clicking on the uninstall.exe in the installation folder will start the uninstall process.

Related News

• Problem downloading software? (16/12/2019)
• Need help designing studies to estimate genetic effective population size? (17/10/2018)

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