Difference between revisions of "RevBayes"

From MolEvol
(Phylogenetic Inference using RevBayes: Substitution Models for Unconstrained Trees)
(Data & Analysis Files)
Line 22: Line 22:
 
* [https://raw.githubusercontent.com/revbayes/revbayes_tutorial/master/RB_CTMC_Tutorial/RevBayes_scripts/GTR_Gamma.nonclock.Rev GTR Analysis File]
 
* [https://raw.githubusercontent.com/revbayes/revbayes_tutorial/master/RB_CTMC_Tutorial/RevBayes_scripts/GTR_Gamma.nonclock.Rev GTR Analysis File]
  
On the course cluster download the data files:
+
==== On the MBL Cluster ====
 +
 
 +
On the course cluster create a directory to run your analysis:
 
<pre>
 
<pre>
wget https://molevol.mbl.edu/images/7/76/RB_BayesFactor_files.tar.gz
+
mkdir RB_tutorial
 +
cd RB_tutorial
 
</pre>
 
</pre>
  
Uncompress the tutorial file directory:
+
Make a directory for the data file:
 
<pre>
 
<pre>
tar xzf RB_BayesFactor_files.tar.gz
+
mkdir data
 
</pre>
 
</pre>
  
Navigate to the tutorial directory:
+
Download the data file to the data directory:
 
<pre>
 
<pre>
cd RB_tutorial_files
+
wget https://raw.githubusercontent.com/revbayes/revbayes_tutorial/master/RB_CTMC_Tutorial/data/primates_cytb.nex data/
 
</pre>
 
</pre>
  
 
Add the RevBayes module:
 
Add the RevBayes module:
 
<pre>
 
<pre>
module load revbayes
+
module load bioware
 
</pre>
 
</pre>
  

Revision as of 15:30, 21 July 2015

Course materials by Tracy Heath, Michael Landis, and Sebastian Höhna on model selection and data partitioning in RevBayes


Lecture

Introduction to RevBayes slides are available on slideshare

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

Data & Analysis Files

On the MBL Cluster

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

mkdir RB_tutorial
cd RB_tutorial

Make a directory for the data file:

mkdir data

Download the data file to the data directory:

wget https://raw.githubusercontent.com/revbayes/revbayes_tutorial/master/RB_CTMC_Tutorial/data/primates_cytb.nex data/

Add the RevBayes module:

module load bioware

Execute RevBayes:

rb

Additional Software