Jambe

Probabilistic Divergence Measures for Detecting Recombination with Markov Chain Monte Carlo

Downloading and compiling the software

• Download the software package by clicking here. This gives you a gzipped TAR file called Jambe.tar.gz. To extract the files under UNIX, proceed as follows:

  gunzip Jambe.tar.gz
tar xvf Jambe.tar

  You can now delete the TAR file:

  rm Jambe.tar

• Prior to compilation you have to edit the file RunBambe.java, where the C++ program BAMBE is invoked. This happens in the line

  proc= myRuntime.exec(new String[] {"/bin/sh", "-c", "/bioss/dh/My_software/Jambe/bambe < infile"});

  which you have to change so as to specify the directory on your system where BAMBE has been installed.

• Compile the Java programs with the command:

  javac NNNN.java

  where NNNN.java are the names of the various Java classes. Note that the software package has been written in Java 1.1. Some of the commands are deprecated and will not run under Java 1.2. You can test if you have the right version of Java installed by typing

  java -version

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  Last modified: February 2002