title: Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST.
abstract: BACKGROUND
  Advances in sequencing technology continue to deliver increasingly large molecular sequence datasets that are often heavily partitioned in order to accurately model the underlying evolutionary processes. In phylogenetic analyses, partitioning strategies involve estimating conditionally independent models of molecular evolution for different genes and different positions within those genes, requiring a large number of evolutionary parameters that have to be estimated, leading to an increased computational burden for such analyses. The past two decades have also seen the rise of multi-core processors, both in the central processing unit (CPU) and Graphics processing unit processor markets, enabling massively parallel computations that are not yet fully exploited by many software packages for multipartite analyses.
  
  
  RESULTS
  We here propose a Markov chain Monte Carlo (MCMC) approach using an adaptive multivariate transition kernel to estimate in parallel a large number of parameters, split across partitioned data, by exploiting multi-core processing. Across several real-world examples, we demonstrate that our approach enables the estimation of these multipartite parameters more efficiently than standard approaches that typically use a mixture of univariate transition kernels. In one case, when estimating the relative rate parameter of the non-coding partition in a heterochronous dataset, MCMC integration efficiency improves by > 14-fold.
  
  
  METHODS
  Our implementation is part of the BEAST code base, a widely used open source software package to perform Bayesian phylogenetic inference.
  
  
  BACKGROUND
  guy.baele@kuleuven.be.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.
authors.forename: Guy
authors.initials: G
authors.lastname: Baele
authors.affiliation: Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.
authors.forename: Philippe
authors.initials: P
authors.lastname: Lemey
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.|Centre for Immunology, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, King's Buildings, Edinburgh, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Rambaut
authors.affiliation: Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.|Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA, USA.|Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
authors.forename: Marc A
authors.initials: MA
authors.lastname: Suchard
mesh_terms: D001499:Bayes Theorem; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D008390:Markov Chains; D009010:Monte Carlo Method; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software