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genesis

Population structure and PCA viewer

August 2021 Updates (bug fixes -- system specific)

Program takes as input output of PCA or admixture programs and allows user to interactively produce publication quality pictures.

  • the manual can be found in the doc directory
  • You need only download the Genesis.jar file which requires Java 1.7 or 1.8.

Run the program like this on an Apple

java -XstartOnFirstThread -jar Genesis.jar

And like this on Windows/Linux

java -jar Genesis.jar

You can download documentation and examples. While you can do all of this individually, you can also get a copy of everything by cloning

git clone https://github.com/shaze/genesis

Making your own version

Download the following platform-independent jars to the src directory

org.eclipse.core.commands-3.10.0.jar org.eclipse.core.runtime-3.7.0.jar batik-all-1.8pre-r1084380.jar org.eclipse.equinox.common-3.15.0.jar itextpdf-5.5.9.jar org.eclipse.jface-3.6.0.jar jfreechart-1.5.3.jar org.w3c.dom.svg-1.1.0.jar jfreesvg-3.4.1.jar

Reasonably similar versions of the above should be fine.

Move to the src directory and do

for j in org.eclipse.core.commands-3.10.0.jar org.eclipse.core.runtime-3.7.0.jar batik-all-1.8pre-r1084380.jar         org.eclipse.equinox.common-3.15.0.jar itextpdf-5.5.9.jar org.eclipse.jface-3.6.0.jar jfreechart-1.5.3.jar org.w3c.dom.svg-1.1.0.jar jfreesvg-3.4.1.jar; do
    jar -xf $x; 
  done

Download the swt.jar specific for your platform to the src directory

run make

I've tested this with Java 8 and Java 11