Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments

We improve on earlier FPT algorithms for computing a rooted maximum agreement forest (MAF) or a maximum acyclic agreement forest (MAAF) of a pair of phylogenetic trees. Their sizes give the subtree-prune-and-regraft (SPR) distance and the hybridization number of the trees, respectively. We introduce new branching rules that reduce the running time of the algorithms from O(3

• Type: Conference
• Year: 2010
• Where: WEA
• Authors: Chris Whidden, Robert G. Beiko, Norbert Zeh
• Keywords: Agreement Forest, Algorithm, Algorithms, Maximum Acyclic Agreement, WEA 2010