Difference between revisions of "RevBayes"

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== Lecture ==  
 
== Lecture ==  
* Introduction to RevBayes slides are available on [http://www.slideshare.net/trayc7/lecture-on-revbayes-at-the-mbl-workshop-on-molecular-evolution slideshare]
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* Introduction to RevBayes slides  
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** Available to view or download on [http://www.slideshare.net/trayc7/lecture-on-revbayes-at-the-mbl-workshop-on-molecular-evolution slideshare]
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** Or download the [phyloworks.org/workshops/RevBayes_lecture_WH.pdf PDF]
 
* RevBayes script for demo: [http://phyloworks.org/workshops/lnorm.Rev lnorm.Rev]
 
* RevBayes script for demo: [http://phyloworks.org/workshops/lnorm.Rev lnorm.Rev]
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== Phylogenetic Inference using RevBayes: Substitution Models for Unconstrained Trees ==
 
== Phylogenetic Inference using RevBayes: Substitution Models for Unconstrained Trees ==

Revision as of 06:44, 23 July 2015

Course materials by Tracy Heath and Michael Landis on substitution models and phylogenetic reconstruction in RevBayes


Lecture

  • Introduction to RevBayes slides
    • Available to view or download on slideshare
    • Or download the [phyloworks.org/workshops/RevBayes_lecture_WH.pdf PDF]
  • RevBayes script for demo: lnorm.Rev


Phylogenetic Inference using RevBayes: Substitution Models for Unconstrained Trees

RevBayes

Software downloads, tutorials, documentation, and other resources can be found on the RevBayes web page: http://revbayes.com

RevBayes source code can be found on GitHub: https://github.com/revbayes/revbayes

Tutorial

The detailed lab practical document can be found here: tutorial PDF

Help files

Online Help Files

  • Search for RevBayes commands in the upper right corner.
  • Filter by command type by (un-)checking boxes.

Data & Analysis Files

On the MBL Cluster

On the course cluster create a directory to run your analysis:

mkdir RB_tutorial
cd RB_tutorial

Download the data directory containing the data file:

wget https://molevol.mbl.edu/images/8/80/Primates.zip

Un-zip the downloaded file (this will create a directory containing the file "primates_cytb.nex"

unzip Primates.zip

Add the bioware module:

module load bioware

Execute RevBayes:

rb

Additional Software