DualBrothers: Recombination Detection Software


Overview

DualBrothers is a recombination detection software based on the dual Multiple Change-Point (MCP) model. This model allows for changes in topology and evolutionary rates across sites in a multiple sequence alignment. We use Bayesian approach together with an MCMC sampling to simulate from the posterior distribution of the dual MCP model parameters. Please, see details of model specification and sampling algorithm in References below.

Update

Version 1.1 is availble. New options are added:
top_breaks: 1 = update, 0 = do not update (default: 1). Excludes topology break-points from the model.
par_breaks: 1 = update, 0 = do not update (default: 1). Excludes substition change-points from the model.
tree_file: file name with trees in Newick format. At least 3 trees are required!
Example of a tree file:
(0,(1,(2,3)))
(0,(2,(1,3)))
(2,(1,(0,3)))
    

Download

Installation Instructions

  1. You'll need a Java Virtual Machine (JVM) in order to run DualBrothers. You can download it as a part of Java Runtime Environment (JRE) at http://java.com/en/download/manual.jsp.
  2. Get Colt libraries for scientific computing at the Colt web-page, Copy the colt.jar file to some directory
    .../coltdir
  3. Download *.tar.gz file. Unzip and untar it:
    gunzip *.tar.gz
    tar -xvf *.tar
        
    Place the *.jar file into a designated directory, let's say
    .../dualdir
  4. You need to let "java" know where the external libraries reside. There are several ways of doing it. Here are two of them:
  5. Run DualBrothers with the following command
    java DualChange <seed> <command file name> <data file> <output file name>
    
    if you set your CLASSPATH

Alternative implementation


Documentation


Supplementary information


References

  1. Minin VN, Dorman KS, Suchard MA.
    Dual multiple change-point model leads to more accurate recombination detection,
    Bioinformatics, 21:3034-3042, 2005.
  2. Suchard MA, Weiss RE, Dorman KS and Sinsheimer JS.
    Inferring spatial phylogenetic variation along nucleotide sequences: a multiple change-point model,
    Journal of the American Statistical Association 98:427-437, 2003.
  3. Suchard MA, Weiss RE, Dorman KS and Sinsheimer JS.
    Oh brother, where art thou? a Bayes factor test for recombination with uncertain heritage,
    Systematic Biology 51:715-728, 2002.

Last modified: Tue Sep 24 12:48:11 PST 2005