Name: breakpoint_calculator
Author: Birte Kehr <birte.kehr@fu-berlin.de>
Maintainer: Birte Kehr <birte.kehr@fu-berlin.de>
License: GPL v3
Copyright: 2012-2013, FU Berlin
Status: stable
Description: Calculates number of pairwise and triplet breakpoints.
 Given a genome alignment consisting of collinear blocks without duplications,
 this application calculates the number of pairwise and triplet hidden
 breakpoints among each pair and triplet of genomes.
 .
 The method computes a median genome for each pair or triplet of genomes
 using a similar approach to Tannier, Zheng, and Sankoff (2009). The approach
 constructs a weighted graph from the order of collinear blocks forming the
 genomes and computes a maximum weight perfect matching. The weight removed
 from the graph to obtain the matching is used as breakpoint distance. From the
 triplet breakpoint distances, the pairwise breakpoint counts are subtracted.
 .
 This application uses the Lemon graph library: 
 http://lemon.cs.elte.hu/trac/lemon
