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
Efficient algorithms for lateral gene transfer problems
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Topological Rearrangements and Local Search Method for Tandem Duplication Trees
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Beyond galled trees: decomposition and computation of galled networks
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
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
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
An evolutionary approach to the inference of phylogenetic networks
PPSN'06 Proceedings of the 9th international conference on Parallel Problem Solving from Nature
Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model
Logic and Program Semantics
The impact of parameterized complexity to interdisciplinary problem solving
The Multivariate Algorithmic Revolution and Beyond
Accounting for gene tree uncertainties improves gene trees and reconciliation inference
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
| Hi-index | 0.00 |
This paper introduces a combinatorial model that incorporates duplication events as well as lateral gene transfer events (a.k.a. horizontal gene transfer events). To the best of our knowledge, this is the first such model containing both of these events. A so-called dt-scenario is used to explain differences between a gene tree T and species trees S. The model is biologically as well as mathematically sound. Among other biological considerations, the model respects the partial order of evolution implied by S by demanding that the dt-scenarios are "acyclic". We present fixed parameter tractable algorithms that count the minimum number of duplications and lateral transfers, and more generally can compute the set of pairs (t,d) where d is the minimum number of duplications required by any explanation that requires t lateral transfers. This allows us to also compute a weighted parsimony score. We also show how gene loss events can be incorporated into our model. We also give an $NP$-completeness proof which suggests that the intractability is due to the demand that the dt-scenarios be acyclic. When this condition is removed, we can show that the problem is computable in polynomial time via dynamic programming. By generating "synthetic" gene and species trees via a birth-death process, we explored the capacity of our algorithms to faithfully reconstruct the actual number of events taken place. The results are positive.