
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of species. An agreement subtree of two evolutionary trees is an evolutionary tree which is also a topological subtree of the two given trees. We give an algorithm to determine the largest possible number of leaves in any agreement subtree of two trees T_1 and T_2 with n leaves each. If the maximum degree d of these trees is bounded by a constant, the time complexity is O(n log^2(n)) and is within a log(n) factor of optimal. For general d, this algorithm runs in O(n d^2 log(d) log^2(n)) time or alternatively in O(n d sqrt(d) log^3(n)) time.
FOS: Computer and information sciences, J.3, evolutionary trees, Analysis of algorithms and problem complexity, Applications of graph theory, Trees, minimal condensed forms, Computational Engineering, Finance, and Science (cs.CE), computational biology, F.2.2; J.3, tree contractions, Graph algorithms (graph-theoretic aspects), Computer Science - Data Structures and Algorithms, agreement subtree, Data Structures and Algorithms (cs.DS), F.2.2, Computer Science - Computational Engineering, Finance, and Science, General biology and biomathematics
FOS: Computer and information sciences, J.3, evolutionary trees, Analysis of algorithms and problem complexity, Applications of graph theory, Trees, minimal condensed forms, Computational Engineering, Finance, and Science (cs.CE), computational biology, F.2.2; J.3, tree contractions, Graph algorithms (graph-theoretic aspects), Computer Science - Data Structures and Algorithms, agreement subtree, Data Structures and Algorithms (cs.DS), F.2.2, Computer Science - Computational Engineering, Finance, and Science, General biology and biomathematics
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