# Phylogenetic Tree Construction Using Markov Chain Monte Carlo

@article{Li2000PhylogeneticTC, title={Phylogenetic Tree Construction Using Markov Chain Monte Carlo}, author={Shuying S. Li and Dennis K. Pearl and Hani Doss}, journal={Journal of the American Statistical Association}, year={2000}, volume={95}, pages={493 - 508} }

Abstract We describe a Bayesian method based on Markov chain simulation to study the phylogenetic relationship in a group of DNA sequences. Under simple models of mutational events, our method produces a Markov chain whose stationary distribution is the conditional distribution of the phylogeny given the observed sequences. Our algorithm strikes a reasonable balance between the desire to move globally through the space of phylogenies and the need to make computationally feasible moves in areas…

## 274 Citations

### Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods

- BiologyBiometrics
- 1999

A Markov chain to sample from the posterior distribution for a phylogenetic tree given sequence information from the corresponding set of organisms is derived, generating reproducible estimates and credible sets for the path of evolution.

### Limitations of Markov chain Monte Carlo algorithms for Bayesian inference of phylogeny

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This paper presents the first theoretical work analyzing the rate of convergence of several Markov chains widely used in phylogenetic inference, and proves that many of the popular Markov Chains take exponentially long to reach their stationary distribution.

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### Markov chain Monte Carlo and its applications to phylogenetic tree construction

- Biology
- 2007

This thesis forms a novel Bayesian model for phylogenetic tree construction based on recent studies that incorporates known information about the evolutionary history of the species, referred to as the species phylogeny, in a statistically rigorous way and develops an inference algorithm based on a Markov chain Monte Carlo method in order to overcome the computational complexity inherent in the problem.

### Phylogenetic MCMC Algorithms Are Misleading on Mixtures of Trees

- BiologyScience
- 2005

It is proved that the Markov chains take an exponentially long number of iterations to converge to the posterior distribution, which means that in cases of data containing potentially conflicting phylogenetic signals, phylogenetic reconstruction should be performed separately on each signal.

### Guided tree topology proposals for Bayesian phylogenetic inference.

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This work investigates the performance of common MCMC proposal distributions in terms of median and variance of run time to convergence on 11 data sets, and introduces two new Metropolized Gibbs Samplers for moving through "tree space".

### Bayesian selection of continuous-time Markov chain evolutionary models.

- BiologyMolecular biology and evolution
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A reversible jump Markov chain Monte Carlo approach to estimating the posterior distribution of phylogenies based on aligned DNA/RNA sequences under several hierarchical evolutionary models is developed and found that the Kimura model is too restrictive, and the Hasegawa, Kishino, and Yano model can be rejected for some data sets.

### Geometric ergodicity of a hybrid sampler for Bayesian inference of phylogenetic branch lengths.

- BiologyMathematical biosciences
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### Markov Chasin Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees

- Computer Science
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We further develop the Bayesian framework for analyzing aligned nucleotide sequence data to reconstruct phylogenies, assess uncertainty in the reconstructions, and perform other statistical…

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