A note on the height of binary search trees
Journal of the ACM (JACM)
Computing with unreliable information
STOC '90 Proceedings of the twenty-second annual ACM symposium on Theory of computing
Randomized algorithms
Determining the evolutionary tree using experiments
Journal of Algorithms
A few logs suffice to build (almost) all trees: part II
Theoretical Computer Science
Computing the quartet distance between evolutionary trees
SODA '00 Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms
On the complexity of distance-based evolutionary tree reconstruction
SODA '03 Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms
Quartet Cleaning: Improved Algorithms and Simulations
ESA '99 Proceedings of the 7th Annual European Symposium on Algorithms
Orchestrating Quartets: Approximation and Data Correction
FOCS '98 Proceedings of the 39th Annual Symposium on Foundations of Computer Science
Quartet-Based Phylogeny Reconstruction with Answer Set Programming
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Noisy binary search and its applications
SODA '07 Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms
Fast and reliable reconstruction of phylogenetic trees with very short edges
Proceedings of the nineteenth annual ACM-SIAM symposium on Discrete algorithms
Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Concentration of Measure for the Analysis of Randomized Algorithms
Concentration of Measure for the Analysis of Randomized Algorithms
Balanced randomized tree splitting with applications to evolutionary tree constructions
STACS'99 Proceedings of the 16th annual conference on Theoretical aspects of computer science
Fast error-tolerant quartet phylogeny algorithms
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Towards a practical O(n log n) phylogeny algorithm
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Theoretical and practical improvements on the RMQ-Problem, with applications to LCA and LCE
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
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We present a quartet-based phylogeny algorithm that returns the correct topology for n taxa in O(nlogn) time with high probability, assuming that each quartet is inconsistent with the true tree topology with constant probability, independent of other quartets. Our incremental algorithm relies upon a search tree structure for the phylogeny that is balanced, with high probability, no matter the true topology. In experiments, our prototype was as fast as the fastest heuristics, but because real data do not typically satisfy our probabilistic assumptions, its overall performance is not as good as our theoretical results predict.