NeEstimator2.X

This repository contain the source code of NeEstimator v2.x software (see NeEstimator software at Molecular Fisheries Laboratory) received from Jennifer Ovenden and maintained by NeEstimator development team until 2019.

This folder contains the source code of NeEstimator v2.x binary software and the java application which wraps the binary software and provide a GUI interface.

Build (linux)

To build all the software, you require JDK 1.8 (at least) and Apache Ant. You can build the binary software simply by:

make

In the project root directory. The binary software will be placed in the same directory. To build the GUI application, you need to enter into NeEstimator2x:

cd NeEstimator2x
ant

this will generate the NeEstimator2x/dist/NeEstimator2x.jar application.

Run (linux)

To use the compiled binary with the GUI application, the binary software must be in the same directory as the GUI application. Place the NeEstimator2x/dist/NeEstimator2x.jar file in the same position of the binary software. Next, the binary software shoud be renamed into Ne2L. For example in the project root directory, you can do like this:

mv Ne2x Ne2L
cp NeEstimator2x/dist/NeEstimator2x.jar .

Then start the GUI application with:

java -jar NeEstimator2x.jar

Citation

If you use this code, 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 V2.1 (Do et al. 2014.).”

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.