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
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
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
An Ω(n2/ log n) speed-up of TBR heuristics for the gene-duplication problem
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Inferring species trees from gene duplication episodes
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Linear-Time Algorithms for the Multiple Gene Duplication Problems
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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
| Hi-index | 0.00 |
The gene-duplication problem is to infer a species supertree from acollection of gene trees that are confounded by complex histories of gene duplicationevents. This problem is NP-complete and thus requires efficient and effectiveheuristics. Existing heuristics perform a stepwise search of the tree space, whereeach step is guided by an exact solution to an instance of a local search problem.A classical local search problem is the NNI search problem, which is based onthe nearest neighbor interchange operation. In this work we (i) provide a novelnear-linear time algorithm for the NNI search problem, (ii) introduce extensionsthat significantly enlarge the search space of the NNI search problem, and (iii)present algorithms for these extended versions that are asymptotically just as efficientas our algorithm for the NNI search problem. The substantially extendedNNI search problem, along with the exceptional speed-up achieved, make thegene-duplication problem more tractable for large-scale phylogenetic analyses.