🧬 NeEstimator v2 Workflow
This guide describes how to install and use NeEstimator v2 to estimate effective population size (Ne) from a Genepop file on macOS (Apple Silicon). Note that the online host of this tool is no longer available, so you have to clone this github repo and build the tool on your own machine.
🔧 Setup Instructions
1. Install Prerequisites
Install SDKMAN and Java 8 (Zulu JDK):
curl -s "https://get.sdkman.io" | bash
source "$HOME/.sdkman/bin/sdkman-init.sh"
sdk install java 8.0.442-zulu
sdk use java 8.0.442-zulu
Install Apache Ant:
brew install ant
2. Download and Build NeEstimator
Clone or download the NeEstimator v2 source code, then run:
cd NeEstimator2.X
make
cd NeEstimator2x
ant
cd ..
mv Ne2x Ne2M
cp NeEstimator2x/dist/NeEstimator2x.jar .
3. Run the GUI
java -jar NeEstimator2x.jar
Make sure Ne2M is in the same directory as the .jar file. Select your Genepop file and configure settings in the GUI. Then click “Run Ne”.
📊 Results Summary
| Population | LD Method Ne | Het. Excess Ne | Molecular Coancestry Ne |
|---|---|---|---|
| CSMB17W.01 | ~3422 – 3926 | 119 – 153 | 13.1 |
| CSMB18H.01 | ~490 – 539 | Infinite | 6.8 |
| NSFB16H.01 | ~333 – 376 | Infinite | 19.8 |
| NSFB18W2.01 | ~1719 – 1903 | Infinite | 23.6 |
| SSNB18H.01 | ~300 – 336 | 464 – 620 | 2.4 |
| SSNB18W.01 | ~3378 – 4046 | Infinite | 9.3 |
📝 Notes
- LD method estimates are generally more stable and preferred for comparisons.
- Heterozygote Excess often returned “Infinite”, suggesting little to no detectable excess.
- Molecular Coancestry consistently yielded very small Ne values, indicating possible recent bottlenecks or high relatedness.