Breakpoint Calculator

Birte Kehr, Knut Reinert, and Aaron Darling


Given a genome alignment without duplications, this application calculates pairwise and three-way hidden breakpoint counts for each pair and triplet of genomes.

Hidden breakpoints of rearrangement are only detectable by comparison of three or more genomes, but exhibit no rearrangements in pairwise comparisons. The pairwise breakpoint counts correspond to the classic breakpoint distance of two genomes.

The breakpoint calculator constructs a weighted graph from the adjacencies of the genomes in the alignment and computes a maximum weight perfect matching. A similar approach was described by Tannier, Zheng, and Sankoff (2009) for median computation. Using the weight of the original graph and the matching weight, the breakpoint calculator determines the breakpoint counts.

Breakpoint Calculator Binaries

Supported platforms are: Windows, Linux 64, and Mac OS X. Please take a look at the README file for usage instructions.


  • Kehr, B., Reinert, K., Darling, A.E. (2012). Hidden breakpoints in genome alignments. WABI 2012.
  • The manuscript describing this work can be found on arXiv at the following address:


For questions, comments, or suggestions please contact Birte Kehr.

Last Update 25. April 2013