How to use RapGreen to reconcile phylogenetic trees

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Jean-François edited this page Dec 1, 2020 · 9 revisions

RapGreen is a very versatile Java package, to manipulate et annotate phylogenetic trees. The main usage of this package remains to reconcile phylogenetic trees with the corresponding species tree.

First of all, download the whole package in your working directory:

git clone https://github.com/SouthGreenPlatform/rap-green.git

Step 1: compile the RapGreen reconciliation facilities

Compile the RapGreen java package (mostly tested in Java 8, but compatible with newer of older versions):

cd rap-green

javac rapgreen/*.java

Or you can choose to directly use the bin/RapGreen.jar executable archive file if you have the same JDK version used to compile this available version, which is JDK8.

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