From Gene Trees to Species Trees
SIAM Journal on Computing
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
DLS-trees: a model of evolutionary scenarios
Theoretical Computer Science
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
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)
Removing noise from gene trees
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Reconciling gene trees with apparent polytomies
COCOON'06 Proceedings of the 12th annual international conference on Computing and Combinatorics
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Reconciliation is a method widely used to infer the evolutionary relationship between the members of a gene family. It consists of comparing a gene tree with a species tree, and interpreting the incongruence between the two trees as evidence of duplication and loss. In the case of binary rooted trees, linear-time algorithms have been developed for the duplication, loss, and mutation (duplication + loss) costs. However, a strict prerequisite to reconciliation is to have a gene tree free from error, as few misplaced edges may lead to a completely different result in terms of the number and position of inferred duplications and losses. How should the weak edges be handled? One reasonable answer is to transform the binary gene tree into a non-binary tree by removing each weak edge and collapsing its two incident vertices into one. The created polytomies are "apparent" as they do not reflect a true simultaneous divergence of many copies from a common ancestor, but rather a lack of resolution. In this paper, we consider the problem of reconciling a non-binary rooted gene tree G with a binary rooted species tree S, were polytomies of G are assumed to be apparent. We give a linear-time algorithm that infers a reconciliation of minimum mutation cost between a binary refinement of a polytomy and S, improving on the best known result, which is cubic. This implies a straightforward generalization to a gene tree G with nodes of arbitrary degree, that runs in time O(|S||G|), which is shown to be an optimal algorithm.