Bayesian Phylogenetics in RevBayes

Location: Workshop on Molecular Evolution at MBL, Woods Hole, MA
Dates: 7/20, 2018 to 7/29, 2018
Instructors: Michael Landis, Tracy Heath, John Huelsenbeck, Paul Lewis
Register: https://molevol.mbl.edu

Description

Instruction in Bayesian phylogenetic inference and divergence-time estimation will be taught at the Workshop on Molecular Evolution at the Marine Biological Laboratory (MBL). This course was founded in 1988 and is the longest-running workshop serving the field of evolutionary biology. Students work closely with internationally-recognized scientists, receiving (i) high-level instruction in the principles of molecular evolution and evolutionary genomics, (ii) advanced training in statistical methods best suited to modern datasets, and (iii) hands-on experience with the latest software tools (often from the authors of the programs they are using). The material is delivered via lectures, discussions, and bioinformatic exercises motivated by contemporary topics in molecular evolution. A hallmark of this workshop is the direct interaction between students and field-leading scientists. The workshop serves graduate students, postdocs, and established faculty from around the world seeking to apply the principles of molecular evolution to questions of anthropology, conservation genetics, development, behavior, physiology, and ecology. The workshop also welcomes participants from federal agencies and science journalists. A priority of this workshop is to foster an environment where students can learn from each other as well from the course faculty.

For the full workshop content, list of faculty, and schedule, please see the main course website.

Instructions for working with the RevBayes tutorials on MBL computing resources are provided in the section on Using RevBayes on the MBL Cluster below.

Software

Before the course starts, please install the following software on your own computer:

Schedule

Date Time Topic Material Instructors
Sunday 09:00-12:00 Lecture: An Introduction to Bayesian Phylogenetics Lecture slides and other materials Paul Lewis
Sunday 12:00-14:00 Lunch
Sunday 14:00-17:00 Lecture: Likelihood-based Phylogenetic Inference Lecture slides and other materials John Huelsenbeck
Sunday 17:00-19:00 Dinner
Sunday 19:00-20:30 Lecture: Phylogenetic Inference and Graphical Models Lecture slides Michael Landis
Sunday 20:30-20:45 Break
Sunday 20:45-22:00 Lecture: Bayesian Divergence-Time Estimation Lecture slides Tracy Heath
Monday 09:00-22:00 See course schedule
Tuesday 09:00-22:00 See course schedule
Wednesday 09:00-22:00 Free Day
Thursday 09:00-22:00 See course schedule
Friday 09:00-22:00 See course schedule
Saturday 09:00-09:30 Lab: Introduction to RevBayes and the Rev Language Lab slides Michael Landis
Saturday 09:30-10:00 Lab: Introduction to RevBayes and the Rev Language Rev Language Syntax Michael Landis
Saturday 10:00-12:00 Lab: Phylogenetic Inference in RevBayes Substitution Models Michael Landis
Saturday 12:00-14:00 Lunch
Saturday 14:00-14:20 Lecture: Bayesian Divergence-Time Estimation, continued Lecture slides Tracy Heath
Saturday 14:20-17:00 Lab: Divergence-Time Estimation in RevBayes Combined-Evidence Analysis and the Fossilized Birth-Death Process for Analysis of Fossil and Extant Specimens Tracy Heath

Using RevBayes on the MBL Cluster

Executing RevBayes

For the tutorials used in this workshop, you may want to use the version of RevBayes on the MBL cluster.

Once you log in, you can use RevBayes from any directory on the cluster by just typing rb.

rb
Build from master (94149b) on Mon Jul 23 15:55:28 EDT 2018

Visit the website www.RevBayes.com for more information about RevBayes.

RevBayes is free software released under the GPL license, version 3. Type 'license()' for details.

To quit RevBayes type 'quit()' or 'q()'.


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Downloading Data Files

Some of the tutorials you will us have data files associated with them. You will find hyperlinks to all of the required files on the tutorial page. These should be listed in the “Data files and scripts” box at the top of the tutorial page below the table of contents.

For this workshop, we recommend that you create a new folder for each tutorial that you work through. Follow the directions in the tutorial for creating your directory structure. Then download the individual files using wget.

For example, in the tutorial on divergence times, you will need to download the sequence data file:

wget https://revbayes.github.io/tutorials/fbd/data/bears_cytb.nex

Writing Rev Scripts

Some tutorials require that you write several modular Rev scripts to define your model and MCMC analysis. We reccomend that you compose these files on your own computer or using the text editor on the MBL cluster. If you create these files on your personal machine, you will have to upload them to the cluster using scp or cyberduck.