# Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method.

@article{Yang1997BayesianPI, title={Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method.}, author={Z Yang and Bruce Rannala}, journal={Molecular biology and evolution}, year={1997}, volume={14 7}, pages={ 717-24 } }

An improved Bayesian method is presented for estimating phylogenetic trees using DNA sequence data. The birth-death process with species sampling is used to specify the prior distribution of phylogenies and ancestral speciation times, and the posterior probabilities of phylogenies are used to estimate the maximum posterior probability (MAP) tree. Monte Carlo integration is used to integrate over the ancestral speciation times for particular trees. A Markov Chain Monte Carlo method is used to…

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## References

SHOWING 1-10 OF 19 REFERENCES

### Monte Carlo Sampling Methods Using Markov Chains and Their Applications

- Mathematics
- 1970

SUMMARY A generalization of the sampling method introduced by Metropolis et al. (1953) is presented along with an exposition of the relevant theory, techniques of application and methods and…

### Gene genealogy in a population of variable size

- MathematicsHeredity
- 1997

The joint distribution of the coalescence times is shown to be invariant in λ and µ, conditional on the current population size, so that exponential growth of a population cannot be distinguished from exponential decline based on the shape of the resulting genealogy.

### Molecular phylogeny and evolution of primate mitochondrial DNA.

- BiologyMolecular biology and evolution
- 1988

A phylogenetic tree for the four groups of primates is constructed and suggests that the rate of nucleotide substitution for mtDNAs in hominines (human, chimpanzee, and gorilla) may have slowed down compared with that for old-world monkeys.

### Bayesian computation via the gibbs sampler and related markov chain monte carlo methods (with discus

- Mathematics
- 1987

The use of the Gibbs sampler for Bayesian computation is reviewed and illustrated in the context of some canonical examples. Other Markov chain Monte Carlo simulation methods are also briefly…

### The reconstructed evolutionary process.

- BiologyPhilosophical transactions of the Royal Society of London. Series B, Biological sciences
- 1994

This work derives probability models for phylogenies reconstructed from contemporary taxa, allowing real data to be compared with specified null models of evolution, and lineage birth and death rates to be estimated.

### Estimation of the Branch Points of a Branching Diffusion Process

- Mathematics
- 1970

A solution to the problem of estimating the positions and times of the branch points of a Brownian-motion/Yule process, given the positions of all the particles at a particular time, is outlined. A…

### The Bayesian choice : a decision-theoretic motivation

- Mathematics, Economics
- 1996

Contents: Introduction.- Decision-Theoretic Foundations of Statistical Inference.- From Prior Information to Prior Distributions.- Bayesian Point Estimation.- Tests and Confidence Regions.-…

### Statistical Decision Theory and Bayesian Analysis

- Computer Science
- 1988

An overview of statistical decision theory, which emphasizes the use and application of the philosophical ideas and mathematical structure of decision theory. The text assumes a knowledge of basic…

### A complete guide to monkeys, apes, and other primates

- Medicine
- 1983

The Cultural Anthropology Panel, benefitting from a larger participation, produced a more solid document, the value of which may be less ephemeral than the others.

### Primates of the World

- Biology
- 1992

The volumes provide clear, basic information on physiology, classification, habitat, life cycle, and behavior, including such diverse topics as courtship and mating, egg-laying and development, reproduction and parental care, food and feeding.