MOTIVATION: We introduce a dual multiple change-point (MCP) model for recombination detection among aligned nucleotide sequences. The dual MCP model is an extension of the model introduced previously by Suchard and co-workers. In the original single MCP model, one change-point process is used to model spatial phylogenetic variation. Here, we show that using two change-point processes, one for spatial variation of tree topologies and the other for spatial variation of substitution process parameters, increases recombination detection accuracy. Statistical analysis is done in a Bayesian framework using reversible jump Markov chain Monte Carlo sampling to approximate the joint posterior distribution of all model parameters. RESULTS: We use primate mitochondrial DNA data with simulated recombination break-points at specific locations to compare the two models. We also analyze two real HIV sequences to identify recombination break-points using the dual MCP model.
MOTIVATION: We introduce a dual multiple change-point (MCP) model for recombination detection among aligned nucleotide sequences. The dual MCP model is an extension of the model introduced previously by Suchard and co-workers. In the original single MCP model, one change-point process is used to model spatial phylogenetic variation. Here, we show that using two change-point processes, one for spatial variation of tree topologies and the other for spatial variation of substitution process parameters, increases recombination detection accuracy. Statistical analysis is done in a Bayesian framework using reversible jump Markov chain Monte Carlo sampling to approximate the joint posterior distribution of all model parameters. RESULTS: We use primate mitochondrial DNA data with simulated recombination break-points at specific locations to compare the two models. We also analyze two real HIV sequences to identify recombination break-points using the dual MCP model.
Authors: Binshan Shi; Christina Kitchen; Barbara Weiser; Douglas Mayers; Brian Foley; Kimdar Kemal; Kathryn Anastos; Marc Suchard; Monica Parker; Cheryl Brunner; Harold Burger Journal: Virology Date: 2010-05-08 Impact factor: 3.616
Authors: Kimdar S Kemal; Christina M Ramirez; Harold Burger; Brian Foley; Douglas Mayers; Thomas Klimkait; François Hamy; Kathryn Anastos; Katarina Petrovic; Vladimir N Minin; Marc A Suchard; Barbara Weiser Journal: AIDS Res Hum Retroviruses Date: 2012-04-10 Impact factor: 2.205
Authors: Jose A Farfan-Ale; Maria A Loroño-Pino; Julian E Garcia-Rejon; Einat Hovav; Ann M Powers; Ming Lin; Karin S Dorman; Kenneth B Platt; Lyric C Bartholomay; Victor Soto; Barry J Beaty; Robert S Lanciotti; Bradley J Blitvich Journal: Am J Trop Med Hyg Date: 2009-01 Impact factor: 2.345