Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers

Authors:
Zhi-Zhong Chen;Fei Deng;Lusheng Wang
Affiliations:
Tokyo Denki University, Hatoyama;City University of Hong Kong, Hong Kong;City University of Hong Kong, Hong Kong
Venue:
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Year:
2012

Citing 13
Cited 1

New algorithms for the duplication-loss model

RECOMB '00 Proceedings of the fourth 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
From Gene Trees to Species Trees

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Reconciliation problems for duplication, loss and horizontal gene transfer

RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Maximum likelihood of phylogenetic networks

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Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion†

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The multiple gene duplication problem revisited

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The gene evolution model and computing its associated probabilities

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An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers

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)
Network model and efficient method for detecting relative duplications or horizontal gene transfers

ICCABS '11 Proceedings of the 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences
RIATA-HGT: a fast and accurate heuristic for reconstructing horizontal gene transfer

COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer

RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology

Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss

RECOMB'13 Proceedings of the 17th international conference on Research in Computational Molecular Biology

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Abstract

We give a fixed-parameter algorithm for the problem of enumerating all minimum-cost LCA-reconciliations involving gene duplications, gene losses, and lateral gene transfers (LGTs) for a given species tree S and a given gene tree G. Our algorithm can work for the weighted version of the problem, where the costs of a gene duplication, a gene loss, and an LGT are left to the user's discretion. The algorithm runs in O(m+3^{k/c} n) time, where m is the number of vertices in S, n is the number of vertices in G, c is the smaller between a gene duplication cost and an LGT cost, and k is the minimum cost of an LCA-reconciliation between S and G. The time complexity is indeed better if the cost of a gene loss is greater than 0. In particular, when the cost of a gene loss is at least 0.614c, the running time of the algorithm is O(m+2.78^{k/c}n).