Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Computing the Local Consensus of Trees
SIAM Journal on Computing
Rank aggregation methods for the Web
Proceedings of the 10th international conference on World Wide Web
Quartet Cleaning: Improved Algorithms and Simulations
ESA '99 Proceedings of the 7th Annual European Symposium on Algorithms
SIAM Journal on Discrete Mathematics
Aggregating inconsistent information: ranking and clustering
Proceedings of the thirty-seventh annual ACM symposium on Theory of computing
Using Max Cut to Enhance Rooted Trees Consistency
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
SIAM Journal on Discrete Mathematics
Optimal evolutionary tree comparison by sparse dynamic programming
SFCS '94 Proceedings of the 35th Annual Symposium on Foundations of Computer Science
An improved algorithm for the maximum agreement subtree problem
Information Processing Letters
New results on optimizing rooted triplets consistency
Discrete Applied Mathematics
Bioinformatics
Quartets MaxCut: A Divide and Conquer Quartets Algorithm
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Computing the rooted triplet distance between galled trees by counting triangles
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
An optimal algorithm for building the majority rule consensus tree
RECOMB'13 Proceedings of the 17th international conference on Research in Computational Molecular Biology
Computing the rooted triplet distance between galled trees by counting triangles
Journal of Discrete Algorithms
| Hi-index | 5.23 |
Partially-resolved-that is, non-binary-trees arise frequently in the analysis of species evolution. Non-binary nodes, also called multifurcations, must be treated carefully, since they can be interpreted as reflecting either lack of information or actual evolutionary history. While several distance measures exist for comparing trees, none of them deal explicitly with this dichotomy. Here we introduce two kinds of distance measures between rooted and unrooted partially-resolved phylogenetic trees over the same set of species; the measures address multifurcations directly. For rooted trees, the measures are based on the topologies the input trees induce on triplets; that is, on three-element subsets of the set of species. For unrooted trees, the measures are based on quartets (four-element subsets). The first class of measures are parametric distances, where there is a parameter that weighs the difference between an unresolved triplet/quartet topology and a resolved one. The second class of measures are based on the Hausdorff distance, where each tree is viewed as a set of all possible ways in which the tree can be refined to eliminate unresolved nodes. We give efficient algorithms for computing parametric distances and give conditions under which Hausdorff distances can be calculated approximately in polynomial time. Additionally, we (i) derive the expected value of the parametric distance between two random trees, (ii) characterize the conditions under which parametric distances are near-metrics or metrics, (iii) study the computational and algorithmic properties of consensus tree methods based on the measures, and (iv) analyze the interrelationships among Hausdorff and parametric distances.