On the complexity of comparing evolutionary trees
Discrete Applied Mathematics - Special volume on computational molecular biology
On distances between phylogenetic trees
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
New algorithms for the duplication-loss model
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Reconciliation problems for duplication, loss and horizontal gene transfer
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
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Traversing the tangle: algorithms and applications for cophylogenetic studies
Journal of Biomedical Informatics - Special issue: Phylogenetic inferencing: Beyond biology
Computing the Hybridization Number of Two Phylogenetic Trees Is Fixed-Parameter Tractable
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Seeing the trees and their branches in the network is hard
Theoretical Computer Science
Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
The Structure of Level-k Phylogenetic Networks
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Efficiently Calculating Evolutionary Tree Measures Using SAT
SAT '09 Proceedings of the 12th International Conference on Theory and Applications of Satisfiability Testing
Natural Computing: an international journal
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
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)
Inapproximability results for the lateral gene transfer problem
ICTCS'05 Proceedings of the 9th Italian conference on Theoretical Computer Science
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
Identifiability issues in phylogeny-based detection of horizontal gene transfer
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model
Logic and Program Semantics
MURPAR: a fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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This paper develops a model for lateral gene transfer events (a.k.a. horizontal gene transfer events) between a set of gene trees T1, T2, …, Tk and a species tree S. To the best of our knowledge, this model possesses a higher degree of biological and mathematical soundness than any other model proposed in the literature. Among other biological considerations, the model respects the partial order of evolution implied by S. Within our model, we identify an activity parameter that measures the number of genes that are allowed to be simultaneously active in the genome of a taxa and show that finding the most parsimonious scenario that reconciles the disagreeing gene trees with the species tree is doable in polynomial time when the activity level and number of transfers are small, but intractable in general. To the best of our knowledge, all other models proposed in the literature assume implicitly that the activity is one. Finally, using a dataset of bacterial gene sequences from [4], our implementations found 5 optimal scenarios; one of which is the scenario proposed by the authors in [4].