cBrother is software for inferring recombination when recombination is rare.  This is a C version of the code originally written in Java and available elsewhere (http://www.biomath.medsch.ucla.edu/msuchard/  ).

Features

• About 20 time faster than the java version
• Estimate recombination using the single multiple change point (SMCP) model [1].
• Estimate recombination using the dual multiple change point (DMCP) model [2].
• Test recombinants with similar mosaic structure (e.g. circulating recombinant forms) for evidence that they result from multiple recombination events, rather than a single recombination event [3].
• Option of relaxing fixed parental relationships.

Download cBrother now

cBrother Manual (includes tutorial)

References

1. Suchard, M. A. & Weiss, R. E. & Dorman, K. S. & Sinsheimer, J. S., Inferring Spatial Phylogenetic Variation Along Nucleotide Sequences: A Multiple Changepoint Model, in 98 J. Am. Stat. Assoc., 462, 427-437 (2003)
2. Suchard, M. A. & Weiss, R. E. & Dorman, K. S. & Sinsheimer, J. S., Oh Brother, Where Art Thou? A Bayes Factor Test for Recombination with Uncertain Heritage, in 51 Syst. Biol., 5, 715-728 (2002)
3. Minin, V. N. & Dorman, K. S. & Fang, F. & Suchard, M. A., Dual Multiple Change-Point Model Leads to More Accurate Recombination Detection, in 21 Bioinformatics, 13, 3034-3042 (2005)
4. Fang, F. & Minin, V. N. & Suchard, M. A. & Dorman, K. S., Bayesian Phylogenetic Models to Identify Independent Recombination Events at Shared Crossover Points, in In prep. (2006)