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
Efficient algorithms for lateral gene transfer problems
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Hunting for Functionally Analogous Genes
FST TCS 2000 Proceedings of the 20th Conference on Foundations of Software Technology and Theoretical Computer Science
Reconciliation problems for duplication, loss and horizontal gene transfer
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Simultaneous identification of duplications and lateral transfers
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Traversing the tangle: algorithms and applications for cophylogenetic studies
Journal of Biomedical Informatics - Special issue: Phylogenetic inferencing: Beyond biology
DLS-trees: a model of evolutionary scenarios
Theoretical Computer Science
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)
From Gene Trees to Species Trees through a Supertree Approach
LATA '09 Proceedings of the 3rd International Conference on Language and Automata Theory and Applications
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
A scalable parallelization of the gene duplication problem
Journal of Parallel and Distributed Computing
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
Inferring a duplication, speciation and loss history from a gene tree
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
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
Whole mirror duplication-random loss model and pattern avoiding permutations
Information Processing Letters
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
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Simultaneous Identification of Duplications and Lateral Gene Transfers
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Building species trees from larger parts of phylogenomic databases
Information and Computation
From Gene Trees to Species Trees II: Species Tree Inference by Minimizing Deep Coalescence Events
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
An improved algorithm for the macro-evolutionary phylogeny problem
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
A hybrid micro-macroevolutionary approach to gene tree reconstruction
RECOMB'05 Proceedings of the 9th 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
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
Algorithms for knowledge-enhanced supertrees
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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
Efficient Algorithms for Knowledge-Enhanced Supertree and Supermatrix Phylogenetic Problems
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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We consider the problem of constructing a species tree given a number of gene trees. In the frameworks introduced by Goodman et al. [3], Page [10], and Guigó, Muchnik, and Smith [5] this is formulated as an optimization problem; namely, that of finding the species tree requiring the minimum number of duplications and/ or losses in order to explain the gene trees.In this paper, we introduce the WIDTH k DUPLICATION-LOSS and WIDTH k DUPLICATION problems. A gene tree has width k w.r.t. a species tree, if the species tree can be reconciled with the gene tree using at most k simultaneously active copies of the gene along its branches. We explain w.r.t. to the underlying biological model, why this width is typically very small in comparison to the total number of duplications and losses. We show polynomial time algorithms for finding optimal species trees having bounded width w.r.t. at least one of the input gene trees. Furthermore, we present the first algorithm for input gene trees that are unrooted. Lastly, we apply our algorithms to a dataset from [5] and show a species tree requiring significantly fewer duplications and fewer duplications/losses than the trees given in the original paper.