A Markov chain Monte Carlo Expectation Maximization Algorithm for Statistical Analysis of DNA Sequence Evolution with Neighbor-Dependent Substitution Rates
- 1 March 2008
- journal article
- Published by Taylor & Francis in Journal of Computational and Graphical Statistics
- Vol. 17 (1) , 138-162
- https://doi.org/10.1198/106186008x289010
Abstract
The evolution of DNA sequences can be described by discrete state continuous time Markov processes on a phylogenetic tree. We consider neighbor-dependent evolutionary models where the instantaneous...Keywords
This publication has 30 references indexed in Scilit:
- Bayesian analysis for reversible Markov chainsThe Annals of Statistics, 2006
- Pseudo-Likelihood Analysis of Codon Substitution Models with Neighbor-Dependent RatesJournal of Computational Biology, 2005
- Statistical Inference for Discretely Observed Markov Jump ProcessesJournal of the Royal Statistical Society Series B: Statistical Methodology, 2005
- Identification and measurement of neighbor-dependent nucleotide substitution processesBioinformatics, 2005
- Ascent-Based Monte Carlo Expectation– MaximizationJournal of the Royal Statistical Society Series B: Statistical Methodology, 2005
- Inferring Nonneutral Evolution from Human-Chimp-Mouse Orthologous Gene TriosScience, 2003
- A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum LikelihoodSystematic Biology, 2003
- Convergence of the Monte Carlo expectation maximization for curved exponential familiesThe Annals of Statistics, 2003
- An expectation maximization algorithm for training hidden substitution models 1 1Edited by F. CohenJournal of Molecular Biology, 2002
- Wide variations in neighbor-dependent substitution ratesJournal of Molecular Biology, 1994