Dual multiple change-point model leads to more accurate recombination detection - PubMed (original) (raw)

. 2005 Jul 1;21(13):3034-42.

doi: 10.1093/bioinformatics/bti459. Epub 2005 May 24.

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Dual multiple change-point model leads to more accurate recombination detection

Vladimir N Minin et al. Bioinformatics. 2005.

Abstract

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.

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