Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining
SODA '01 Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms
Optimal algorithms for local vertex quartet cleaning
Proceedings of the 2002 ACM symposium on Applied computing
Approximating minimum quartet inconsistency: (abstract)
SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
Minimum Quartet Inconsistency Is Fixed Parameter Tractable
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Reconstructing optimal phylogenetic trees: a challenge in experimental algorithmics
Experimental algorithmics
A fixed-parameter algorithm for minimum quartet inconsistency
Journal of Computer and System Sciences - Special issue on Parameterized computation and complexity
Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining
Journal of Algorithms - Special issue: Twelfth annual ACM-SIAM symposium on discrete algorithms
Algorithms for combining rooted triplets into a galled phylogenetic network
SODA '05 Proceedings of the sixteenth annual ACM-SIAM symposium on Discrete algorithms
Algorithmic Clustering of Music Based on String Compression
Computer Music Journal
Inferring a level-1 phylogenetic network from a dense set of rooted triplets
Theoretical Computer Science - Computing and combinatorics
A polynomial time algorithm for the minimum quartet inconsistency problem with O(n) quartet errors
Information Processing Letters
On the Approximation of Correlation Clustering and Consensus Clustering
Journal of Computer and System Sciences
Constructing Level-2 Phylogenetic Networks from Triplets
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
New results on optimizing rooted triplets consistency
Discrete Applied Mathematics
New fixed-parameter algorithms for the minimum quartet inconsistency problem
IWPEC'08 Proceedings of the 3rd international conference on Parameterized and exact computation
Constructing level-2 phylogenetic networks from triplets
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
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
A Fast Quartet tree heuristic for hierarchical clustering
Pattern Recognition
Topology discovery of sparse random graphs with few participants
Proceedings of the ACM SIGMETRICS joint international conference on Measurement and modeling of computer systems
Topology discovery of sparse random graphs with few participants
ACM SIGMETRICS Performance Evaluation Review - Performance evaluation review
Learning Latent Tree Graphical Models
The Journal of Machine Learning Research
A linear time approximation scheme for maximum quartet consistency on sparse sampled inputs
APPROX'11/RANDOM'11 Proceedings of the 14th international workshop and 15th international conference on Approximation, randomization, and combinatorial optimization: algorithms and techniques
Quartet-based phylogeny reconstruction from gene orders
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
A lookahead branch-and-bound algorithm for the maximum quartet consistency problem
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Triangle-Free outerplanar 3-graphs are pairwise compatibility graphs
WALCOM'12 Proceedings of the 6th international conference on Algorithms and computation
Proceedings of the 27th Annual ACM Symposium on Applied Computing
A Linear Time Approximation Scheme for Maximum Quartet Consistency on Sparse Sampled Inputs
SIAM Journal on Discrete Mathematics
Testing consistency of quartet topologies: A parameterized approach
Information Processing Letters
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Inferring evolutionary trees has long been a challenging problem for both 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. 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.