ch 5 phylogenic　　Prediction　生物信息学教材 研究生用.ppt

* Maximum Likelihood Disadvantages: Computationally intensive Can only be done for a handful of sequences Bayesian Inference Both observed data and parameters of models are random variables Setting up the joint distribution Topology Branch length Parameter of models * When data D is known, Bayes theory gives: Posterior probability likelihood Prior probability Unconditional Probability of data Bayesian Inference-2 Having the posterior probability distribution , we can compute the marginal probability of T as: * P(T|D) can be interpreted as the probability of the tree is correct We need to do at least two things: Approximate the posterior probability distribution Evaluate the integral for P(T|D) These can be done via Markov Chain Monte Carlo Method Markov chain Monte Carlo (MCMC) The basic idea of MCMC is: To construct a Markov chain such that: Have the parameters as the state space, and the stationary distribution –定常分布 is the posterior probability distribution of the parameters Markov chain Monte Carlo (MCMC) Simulate the chain Treat the realization as a sample from the posterior probability distribution MCMC = sampling + continue search * Bayesian phylogenetic inference Phylogenetic tree DNA Data Evolutionary model Likelihood Prior probability Posterior prob. MCMC Starting tree Proposal A sequence of Samples inference Approximate the distribution Bayesian vs ML Maximum likelihood vs. Bayesian estimation Maximum likelihood search for tree that maximizes the chance of seeing the data (P (Data | Tree)) Bayesian inference search for tree that maximizes the chance of seeing the tree given the data (P (Tree | Data)) Comparison of Methods Conclusions The estimation of phylogenies has become a regular step in the analysis of new gene sequences. Still too early to tell if Bayesian approaches will revolutionize tree estimation in general, but it is already clear that MCMC-based approaches are extending the field by answering previously intractable questions 难题. * Which