New algorithms for the duplication-loss model
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
A supertree method for rooted trees
Discrete Applied Mathematics
From Gene Trees to Species Trees
SIAM Journal on Computing
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Reconciling a gene tree to a species tree under the duplication cost model
Theoretical Computer Science
DLS-trees: a model of evolutionary scenarios
Theoretical Computer Science
Using Max Cut to Enhance Rooted Trees Consistency
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
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
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
Removing noise from gene trees
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
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
Minimum leaf removal for reconciliation: complexity and algorithms
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
An optimal reconciliation algorithm for gene trees with polytomies
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Gene tree correction for reconciliation and species tree inference: Complexity and algorithms
Journal of Discrete Algorithms
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Reconciliation between a set of gene trees and a species tree is the most commonly used approach to infer the duplication and loss events in the evolution of gene families, given a species tree. When a species tree is not known, a natural algorithmic problem is to infer a species tree such that the corresponding reconciliation minimizes the number of duplications and/or losses. In this paper, we clarify several theoretical questions and study various algorithmic issues related to these two problems. (1) For a given gene tree T and species tree S , we show that there is a single history explaining T and consistent with S that minimizes gene losses, and that this history also minimizes the number of duplications. We describe a simple linear-time and space algorithm to compute this parsimonious history, that is not based on the Lowest Common Ancestor (LCA) mapping approach; (2) We show that the problem of computing a species tree that minimizes the number of gene duplications, given a set of gene trees, is in fact a slight variant of a supertree problem; (3) We show that deciding if a set of gene trees can be explained using only apparent duplications can be done efficiently, as well as computing a parsimonious species tree for such gene trees. We also characterize gene trees that can be explained using only apparent duplications in terms of compatible triplets of leaves.