W4L1 Inferring phylogeny.pdf

Character support will tend to be recovered in most

Info icon This preview shows pages 11–13. Sign up to view the full content.

character support will tend to be recovered in most replicates. Clade with weak support will not How to estimate clade support Bootstrapping
Image of page 11

Info icon This preview has intentionally blurred sections. Sign up to view the full version.

306 Bayesian Inference ! ! !"" !"#" = ! !"#" !"## ! ( !"## ) ! ( !"#" ) Likelihood Prior probability of the tree, before we collected our data Probability of the data: simply put, this is a normalizing constant that makes all the probabilities sum to 1 Posterior probability As with likelihood & parsimony, heuristic methods need to be used to find the most probable tree 307 Majority-rule consensus tree Fig. 4.30 Bayesian Inference Posterior Probability - Huge numbers of trees are sampled in a Bayesian analysis using a type of heuristic search known as Markov Chain Monte Carlo - The frequency that a node is present in a posterior distribution is its posterior probability . Values between 0.95 and 1 are good. Bayes’ Theorem - Bayesian analysis gives us the probability of the tree, whereas ML gives us the probability of the data given a tree - Why avoid Bayes’ theorem? 1. Usually we don’t know the prior probabilities - Is it OK to use a prior that is uninformative? 2. The normalizing constant in the denominator is very difficult to compute. Mathematical tricks are needed. 3. In practice, Bayesian analysis works very well, and is very commonly used to infer phylogeny 308
Image of page 12
The End 309
Image of page 13
This is the end of the preview. Sign up to access the rest of the document.
  • Spring '18
  • outgroup, tree making

{[ snackBarMessage ]}

What students are saying

  • Left Quote Icon

    As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

    Student Picture

    Kiran Temple University Fox School of Business ‘17, Course Hero Intern

  • Left Quote Icon

    I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

    Student Picture

    Dana University of Pennsylvania ‘17, Course Hero Intern

  • Left Quote Icon

    The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

    Student Picture

    Jill Tulane University ‘16, Course Hero Intern