Lower Bounds for Maximum Parsimony with Gene Order Data

@inproceedings{Bachrach2005LowerBF,
  title={Lower Bounds for Maximum Parsimony with Gene Order Data},
  author={Abraham Bachrach and Kevin C. Chen and Chris Harrelson and Radu Mihaescu and Satish Rao and Apurva Shah},
  booktitle={Comparative Genomics},
  year={2005}
}
In this paper, we study lower bound techniques for branchand-bound algorithms for maximum parsimony, with a focus on gene order data. We give a simple O(n) time dynamic programming algorithm for computing the maximum circular ordering lower bound, where n is the number of leaves. The well-known gene order phylogeny program, GRAPPA, currently implements two heuristic approximations to this lower bounds. Our experiments show a significant improvement over both these methods in practice. Next, we… CONTINUE READING