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
SIAM Journal on Computing
On the Multiple Gene Duplication Problem
ISAAC '98 Proceedings of the 9th International Symposium on Algorithms and Computation
Reconciliation problems for duplication, loss and horizontal gene transfer
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Reconstructing reticulate evolution in species: theory and practice
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
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
Inferring phylogeny from whole genomes
Bioinformatics
URec: a system for unrooted reconciliation
Bioinformatics
The multiple gene duplication problem revisited
Bioinformatics
The gene evolution model and computing its associated probabilities
Journal of the ACM (JACM)
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
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
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
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
Detecting highways of horizontal gene transfer
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
A linear time algorithm for error-corrected reconciliation of unrooted gene trees
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
Reconciling gene trees with apparent polytomies
COCOON'06 Proceedings of the 12th annual international conference on Computing and Combinatorics
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
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An H-tree is a formal model of evolutionary scenario. It can be used to represent any processes with gene duplication and loss, horizontal gene transfer (HGT) and speciation events. The model of H-trees, introduced in [26], is an extension of the duplication-loss model (DL-model). Similarly to its ancestor, it has a number of interesting mathematical and biological properties. It is, however, more computationally complex than the DL-model. In this paper, we primarily address the problem of inferring H-trees that are compatible with a given gene tree and a given phylogeny of species with HGTs. These results create a mathematical and computational foundation for a more general and practical problem of inferring HGTs from given gene and species trees with HGTs. We also demonstrate how our model can be used to support HGT hypotheses based on empirical data sets.