Faster reliable phylogenetic analysis
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
Recovering branches on the tree of life: an approximation algorithm
Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
SODA '00 Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms
Maximum likelihood on four taxa phylogenetic trees: analytic solutions
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Quartet Cleaning: Improved Algorithms and Simulations
ESA '99 Proceedings of the 7th Annual European Symposium on Algorithms
A fixed-parameter algorithm for minimum quartet inconsistency
Journal of Computer and System Sciences - Special issue on Parameterized computation and complexity
Selecting the branches for an evolutionary tree: a polynomial time approximation scheme
Journal of Algorithms
A polynomial time algorithm for the minimum quartet inconsistency problem with O(n) quartet errors
Information Processing Letters
Quartet-Based Phylogeny Reconstruction with Answer Set Programming
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Robustness of Topological Supertree Methods for Reconciling Dense Incompatible Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Reconstructing approximate phylogenetic trees from quartet samples
SODA '10 Proceedings of the twenty-first annual ACM-SIAM symposium on Discrete Algorithms
An experimental study of quartets MaxCut and other supertree methods
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Combinatorial Optimization Solutions for the Maximum Quartet Consistency Problem
Fundamenta Informaticae - RCRA 2008 Experimental Evaluation of Algorithms for Solving Problems with Combinatorial Explosion
Parallel implementation of a quartet-based algorithm for phylogenetic analysis
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Fast error-tolerant quartet phylogeny algorithms
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Phylogenetic tree reconstruction with protein linkage
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Fast error-tolerant quartet phylogeny algorithms
Theoretical Computer Science
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Inferring evolutionary trees has long been a challenging problem both for biologists and computer scientists. In recent years research has concentrated on the quartet method paradigm for inferring evolutionary trees. Quartet methods proceed by first inferring the evolutionary history for every set of four species (resulting in a set Q of inferred quartet topologies) and then recombining these inferred quartet topologies to form an evolutionary tree. This paper presents two results on the quartet method paradigm. The first is a polynomial time approximation scheme (PTAS) for recombining the inferred quartet topologies optimally. This is an important result since, to date, there have been no polynomial time algorithms with performance guarantees for quartet methods. In fact, this is the first known PTAS for inferring evolutionary trees under any paradigm. To achieve this result the natural denseness of the set Q is exploited. The second result is a new technique, called quartet cleaning, that detects and corrects errors in the set Q with performance guarantees. This result has particular significance since quartet methods are usually very sensitive to errors in the data. It is shown how quartet cleaning can dramatically increase the accuracy of quartet methods.