RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer

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, show...

• Type: Conference
• Year: 2005
• Where: COCOON
• Authors: Luay Nakhleh, Derek A. Ruths, Li-San Wang
• Keywords: COCOON 2005, Empirical Performance, Gene Trees, HGT Events