DCJ2HP is written in Java 1.6. You do not need to install the program, on the other hand, you need a Java Virtual Machine (JVM) 1.6 or higher. If you do not have such JVM installed onto your computer, please, visit www.sun.com for a free download.

Please, download the program from here: dcj2hp.tar.gz. Once you have downloaded the compressed file and uncompressed it, you can run the program from command line. To do so, please, change directory to bin/, and type

The s/d flag sets if single or duplicated genomes are read. The syntheny blocks in simple genomes should be consecutively numbered starting from 1, each line should contain one chromosome. See data/halved_ancestor.genome for an example.The syntheny blocks in duplicated genomes should be numbered with 1a, 1b, 2a, 2b, etc. See data/duplicated_ancestor.genome for an example.

file1 and file2 are the two files containing the start and the end genome.

burnin_steps, samples and repeats_between_two_samples are the number of burnin steps, number of samples sampled after the burn-in phase of the MCMC and the number of MCMC steps between two samples.

number_of_parallel_chains is the number of parallel MCMC chains. Finally, s is the parameter defining the temperatures of the chains. The inverse temperature of the k^th is defined as

The output of the MCMC run is written onto the standard output, which might be pielined for further analyses.