David A. Bader
IEEE Fellow
AAAS Fellow
College of Computing
Georgia Tech
Atlanta, GA 30332



A New Implementation and Detailed Study of Breakpoint Analysis

Phylogenies derived from gene order data may prove crucial in answering some fundamental open questions in biomolecular evolution. Yet very few techniques are available for such phylogenetic reconstructions. One method is breakpoint analysis, developed by Blanchette and Sankoff for solving the ``breakpoint phylogeny.''

Our earlier studies confirmed the usefulness of this approach, but also found that BPAnalysis, the implementation developed by Sankoff and Blanchette, was too slow to use on all but very small datasets. We report here on a reimplementation of BPAnalysis using the principles of algorithmic engineering. Our faster (by 2 to 3 orders of magnitude) and flexible implementation allowed us to conduct studies on the characteristics of breakpoint analysis, in terms of running time, quality, and robustness, as well as to analyze datasets that had so far been considered out of reach. We report on these findings and also discuss future directions for our new implementation.

Publication History

Versions of this paper appeared as:
  1. B.M.E. Moret, S. Wyman, D.A. Bader, T. Warnow, M. Yan, ``A New Implementation and Detailed Study of Breakpoint Analysis,'' presented at the Sixth Pacific Symposium on Biocomputing 2001 (PSB2001), Big Island, Hawaii, January 2001.

Download this report in Adobe PDF

The code accompanying this paper can be found here: GRAPPA-1.01.tar.gz


Last updated: July 25, 2004


Computational Biology

Parallel Computing