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

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.
Get Colt libraries for scientific computing at the Colt web-page, Copy the colt.jar file to some directory
```
.../coltdir
```
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
```
You need to let "java" know where the external libraries reside. There are several ways of doing it. Here are two of them:
- Create an environmental variable
```
CLASSPATH=...coltdir/colt.jar:...dualdir/DualBrothers.jar:/other libraries that you use/
```
  . Creating and changing environmental variables is system and shell dependent. For example, in Linux bash shell you need to type
```
export CLASSPATH=$CLASSPATH:.../coltdir/colt.jar:.../dualdir/DualBrothers.jar
```
  in your terminal window or in the .bashrc file of your home directory.
- Alternatively, you can use "-cp" option of the java command, e.g.
```
java -cp .../coltdir/colt.jar:...dualdir/DualBrothers.jar <program name> <program arguments>
```

Run DualBrothers with the following command

java DualChange <seed> <command file name> <data file> <output file name>

if you set your CLASSPATH

Alternative implementation

cBrother is a C version of DualBrothers developed by Karin Dorman's group. cBrother implements additional priors for testing whether recombinant sequences with similar structure resulted from a single or multiple recombination events.

Documentation

Supplementary information

Sequence alignments used in reference (1).
Pure subtype A alignment and figure with the plot of posterior probabilities of phylogenetic trees.
Results of a sensitivity analysis for the number substitution change-points to the choice of prior.

References

Minin VN, Dorman KS, Suchard MA.
Dual multiple change-point model leads to more accurate recombination detection,
Bioinformatics, 21:3034-3042, 2005.
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.
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