Fast algorithms for finding nearest common ancestors
SIAM Journal on Computing
On reconstructing species trees from gene trees in term of duplications and losses
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
New algorithms for the duplication-loss model
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Gene Trees and Species Trees: The Gene-Duplication Problem in Fixed-Parameter Tractable
WADS '99 Proceedings of the 6th International Workshop on Algorithms and Data Structures
LATIN '00 Proceedings of the 4th Latin American Symposium on Theoretical Informatics
Analogs and Duals of teh MAST Problem for Sequences and Trees
ESA '98 Proceedings of the 6th Annual European Symposium on Algorithms
Reconciling gene trees to a species tree
CIAC'03 Proceedings of the 5th Italian conference on Algorithms and complexity
Heuristics for the gene-duplication problem: a Θ(n) speed-up for the local search
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
On the structure of reconciliations
RCG'04 Proceedings of the 2004 RECOMB international conference on Comparative Genomics
A scalable parallelization of the gene duplication problem
Journal of Parallel and Distributed Computing
The gene-duplication problem: near-linear time algorithms for NNI based local searches
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
Inferring species trees from gene duplication episodes
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
H-trees: a Model of Evolutionary Scenarios with Horizontal Gene Transfer
Fundamenta Informaticae - From Mathematical Beauty to the Truth of Nature: to Jerzy Tiuryn on his 60th Birthday
Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model
Logic and Program Semantics
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The gene-duplication problem is to infer a species supertree from gene trees that are confounded by complex histories of gene duplications. This problem is NP-hard and thus requires efficient and effective heuristics. Existing heuristics perform a stepwise search of the tree space, where each step is guided by an exact solution to an instance of a local search problem. We improve on the time complexity of the local search problem by a factor of n2/ log n, where n is the size of the resulting species supertree. Typically, several thousand instances of the local search problem are solved throughout a stepwise heuristic search. Hence, our improvement makes the gene-duplication problem much more tractable for large-scale phylogenetic analyses.