Efficient algorithms for lateral gene transfer problems
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Reconstructing reticulate evolution in species: theory and practice
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)
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
Efficiently Calculating Evolutionary Tree Measures Using SAT
SAT '09 Proceedings of the 12th International Conference on Theory and Applications of Satisfiability Testing
Fixed-Parameter Tractability of the Maximum Agreement Supertree Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Natural Computing: an international journal
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)
Metrics on Multilabeled Trees: Interrelationships and Diameter Bounds
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Identifiability issues in phylogeny-based detection of horizontal gene transfer
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
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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Horizontal gene transfer (HGT) plays a major role in microbial genome diversification, and is claimed to be rampant among various groups of genes in bacteria. Further, HGT is a major confounding factor for any attempt to reconstruct bacterial phylogenies. As a result, detecting and reconstructing HGT events in groups of organisms has become a major endeavor in biology. The problem of detecting HGT events based on incongruence between a species tree and a gene tree is computationally very hard (NP-hard). Efficient algorithms exist for solving restricted cases of the problem. We propose RIATA-HGT, the first polynomial-time heuristic to handle all HGT scenarios, without any restrictions. The method accurately infers HGT events based on analyzing incongruence among species and gene trees. Empirical performance of the method on synthetic and biological data is outstanding. Being a heuristic, RIATA-HGT may overestimate the optimal number of HGT events; empirical performance, however, shows that such overestimation is very mild. We have implemented our method and run it on biological and synthetic data. The results we obtained demonstrate very high accuracy of the method. Current version of RIATA-HGT uses the PAUP tool, and we are in the process of implementing a stand-alone version, with a graphical user interface, which will be made public. The tool, in its current implementation, is available from the authors upon request.