Jambe

Get started with a worked example

1. Copy the data into file dna.dat and make sure the file has the right format. If there are gaps in the alignment, you are advised to transform the file into an ungapped alignment first. This ensures that a window of length L actually contains L nucleotides. Otherwise, gaps are removed internally by BAMBE, which could imply that the effective size of your window varies. To remove gaps, use the Java class RemoveGaps.java. In UNIX, this is done with the following commands:

   java RemoveGaps
mv dna.dat dna_original_alignment.dat
mv dna_no_gaps.dat dna.dat

   Now, dna_original_alignment.dat contains the original alignment with gaps, and dna.dat contains the new ungapped alignment. A new file called gapSites.out lists all the sites in the original alignment that have been discarded.

2. The topologies sampled during the simulation are appended to file resultsAllTopos.out. This requires you to create an empty file with this name first.

3. Create the file in, where you specify the length and the step size of the moving window.

4. Create the file infile, in which you set the parameters of the MCMC simulation.

5. Start the program with the following command:

   java Jambe

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Last modified: February 2002