Maximum likelihood of phylogenetic networks.
BACKGROUND
Horizontal gene transfer (HGT) is believed to be ubiquitous among bacteria, and plays a major role in their genome diversification as well as their ability to develop resistance to antibiotics. In light of its evolutionary significance and implications for human health, developing accurate and efficient methods for detecting and reconstructing HGT is imperative.


RESULTS
In this article we provide a new HGT-oriented likelihood framework for many problems that involve phylogeny-based HGT detection and reconstruction. Beside the formulation of various likelihood criteria, we show that most of these problems are NP-hard, and offer heuristics for efficient and accurate reconstruction of HGT under these criteria. We implemented our heuristics and used them to analyze biological as well as synthetic data. In both cases, our criteria and heuristics exhibited very good performance with respect to identifying the correct number of HGT events as well as inferring their correct location on the species tree.


BACKGROUND
Implementation of the criteria as well as heuristics and hardness proofs are available from the authors upon request. Hardness proofs can also be downloaded at http://www.cs.tau.ac.il/~tamirtul/MLNET/Supp-ML.pdf
Jin
Guohua
G
Department of Computer Science, Rice University Houston, TX, USA.
Nakhleh
Luay
L
Snir
Sagi
S
Tuller
Tamir
T
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D019143:Evolution, Molecular; D005828:Genetics, Population; D016013:Likelihood Functions; D008957:Models, Genetic; D015233:Models, Statistical; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*