From four-taxon trees to phylogenies (preliminary report): the case of mammalian evolution
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
Constructing Big Trees from Short Sequences
ICALP '97 Proceedings of the 24th International Colloquium on Automata, Languages and Programming
Inferring Evolutionary Trees with Strong Combinatorial Evidence
COCOON '97 Proceedings of the Third Annual International Conference on Computing and Combinatorics
Orchestrating Quartets: Approximation and Data Correction
FOCS '98 Proceedings of the 39th Annual Symposium on Foundations of Computer Science
Faster reliable phylogenetic analysis
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
SODA '00 Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms
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
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
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)
Consistency of the QNet algorithm for generating planar split networks from weighted quartets
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
Comparing and aggregating partially resolved trees
LATIN'08 Proceedings of the 8th Latin American conference on Theoretical informatics
A Fast Quartet tree heuristic for hierarchical clustering
Pattern Recognition
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
Comparing and aggregating partially resolved trees
Theoretical Computer Science
The Complexity of Finding Multiple Solutions to Betweenness and Quartet Compatibility
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Application of smodels in quartet based phylogeny construction
LPNMR'05 Proceedings of the 8th international conference on Logic Programming and Nonmonotonic Reasoning
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
A Linear Time Approximation Scheme for Maximum Quartet Consistency on Sparse Sampled Inputs
SIAM Journal on Discrete Mathematics
Fast error-tolerant quartet phylogeny algorithms
Theoretical Computer Science
Testing consistency of quartet topologies: A parameterized approach
Information Processing Letters
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Acritical step in all quartet methods for constructing evolutionary trees is the inference of the topology for each set of four sequences (i.e. quartet). It is a well-known fact that all quartet topology inference methods make mistakes that result in the incorrect inference of quartet topology. These mistakes are called quartet errors. In this paper, two efficient algorithms for correcting bounded numbers of quartet errors are presented. These "quartet cleaning" algorithms are shown to be optimal in that no algorithm can correct more quartet errors. An extensive simulation study reveals that sets of quartet topologies inferred by three popular methods (Neighbor Joining [15], Ordinal Quartet [14] and Maximum Parsimony [10]) almost always contain quartet errors and that a large portion of these quartet errors are corrected by the quartet cleaning algorithms.