On distances between phylogenetic trees
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
New algorithms for the duplication-loss model
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
From Gene Trees to Species Trees
SIAM Journal on Computing
LATIN '00 Proceedings of the 4th Latin American Symposium on Theoretical Informatics
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
On contract-and-refine transformations between phylogenetic trees
SODA '04 Proceedings of the fifteenth annual ACM-SIAM symposium on Discrete algorithms
Reconciling a gene tree to a species tree under the duplication cost model
Theoretical Computer Science
Bioinformatics
An Ω(n^2/ log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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
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
On the structure of reconciliations
RCG'04 Proceedings of the 2004 RECOMB international conference on Comparative Genomics
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
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Complexity insights of the minimum duplication problem
SOFSEM'12 Proceedings of the 38th international conference on Current Trends in Theory and Practice of Computer Science
Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model
Logic and Program Semantics
GTP supertrees from unrooted gene trees: linear time algorithms for NNI based local searches
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Efficient Algorithms for Knowledge-Enhanced Supertree and Supermatrix Phylogenetic Problems
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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The gene-duplication problem is to infer a species supertree from a collection of gene trees that are confounded by complex histories of gene-duplication events. This problem is NP-complete 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. A classical local search problem is the {\tt NNI} search problem, which is based on the nearest neighbor interchange operation. In this work, we 1) provide a novel near-linear time algorithm for the {\tt NNI} search problem, 2) introduce extensions that significantly enlarge the search space of the {\tt NNI} search problem, and 3) present algorithms for these extended versions that are asymptotically just as efficient as our algorithm for the {\tt NNI} search problem. The exceptional speedup achieved in the extended {\tt NNI} search problems makes the gene-duplication problem more tractable for large-scale phylogenetic analyses. We verify the performance of our algorithms in a comparison study using sets of large randomly generated gene trees.