Kaikoura tree theorems: computing the maximum agreement subtree
Information Processing Letters
Maximum Agreement Subtree in a Set of Evolutionary Trees: Metrics and Efficient Algorithms
SIAM Journal on Computing
An O(nlog n) Algorithm for the Maximum Agreement Subtree Problem for Binary Trees
SIAM Journal on Computing
From Gene Trees to Species Trees
SIAM Journal on Computing
Simultaneous identification of duplications and lateral transfers
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
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
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)
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 is the commonly used method for inferring the evolutionary scenario for a gene family. It consists in "embedding" an inferred gene tree into a known species tree, revealing the evolution of the gene family by duplications and losses. The main complaint about reconciliation is that the inferred evolutionary scenario is strongly dependant on the considered gene tree, as few misplaced leaves may lead to a completely different history, with significantly more duplications and losses. As using different phylogenetic methods with different parameters may lead to different gene trees, it is essential to have criteria to choose, among those, the appropriate one for reconciliation. In this paper, following the conclusion of a previous paper, we flag certain duplication vertices of a gene tree, the "non-apparent duplication" (NAD) vertices, as resulting from the misplacement of leaves, and consider the optimization problem of removing the minimum number of leaves leading to a tree without any NAD vertex. We develop a polynomial-time algorithm that is exact for two special classes of gene trees, and show a good performance on simulated data sets in the general case.