The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches

@article{Bansal2008TheGP,
  title={The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches},
  author={Mukul S. Bansal and Oliver Eulenstein},
  journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  year={2008},
  volume={6},
  pages={221-231}
}
The gene-duplication problem is to infer a species supertree from a collection of gene trees that are confounded by complex histories of gene-duplication events. This problem is NP-complete and thus requires efficient and effective heuristics. Existing heuristics perform a stepwise search of the tree space, where each step is guided by an exact solution to an instance of a local search problem. A classical local search problem is the {\tt NNI} search problem, which is based on the nearest… CONTINUE READING