Difference between revisions of "Total-evidence analysis in RevBayes"

From MolEvol
(Getting Started)
Line 16: Line 16:
 
==== Get the Data Files ====
 
==== Get the Data Files ====
  
 +
On the course cluster, create a new directory for the tutorial analysis:
 +
<pre>
 +
mkdir RB_TotalEvidenceDating_FBD_Tutorial
 +
</pre>
  
 +
Move to that directory:
 +
<pre>
 +
cd RB_TotalEvidenceDating_FBD_Tutorial
 +
</pre>
  
==== Running RevBayes on the MBL Cluster ====
+
Get the data files:
 +
<pre>
 +
wget https://github.com/revbayes/revbayes_tutorial/raw/master/RB_TotalEvidenceDating_FBD_Tutorial/data.zip
 +
</pre>
  
On the course cluster, make a copy of the lab directory for your analysis:
+
Unzip the data folder:
 
<pre>
 
<pre>
cp -R /class/molevol-software/revbayes_lab/ .
+
unzip data.zip
 
</pre>
 
</pre>
  
Enter your new copy of the lab directory:
+
Create a directory to hold your RevBayes scripts:
 
<pre>
 
<pre>
cd revbayes_lab
+
mkdir scripts
 
</pre>
 
</pre>
  
Execute RevBayes:
+
==== Running RevBayes on the MBL Cluster ====
 +
 
 +
Execute RevBayes while inside RB_TotalEvidenceDating_FBD_Tutorial:
 
<pre>
 
<pre>
 
rb
 
rb
 
</pre>
 
</pre>

Revision as of 16:52, 24 July 2017

This tutorial was developed for RevBayes workshops and users at home. Here you will find instructions for getting the files and for executing RevBayes on the MBL servers.


Background Reading

  • Höhna et al. 2016. RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language. Systematic Biology, 65:726-736. (PDF)
  • Höhna et al. 2014. Probabilistic graphical model representation in phylogenetics. Systematic Biology 63:753–771. (PDF)

Tutorial PDF

  • The detailed tutorial on the RevBayes repository: download

Getting Started

For this tutorial, most of the work can be completed on your own machines using your favorite text editor. Then, you need to move the script files you create to the MBL cluster and get the data files.

Get the Data Files

On the course cluster, create a new directory for the tutorial analysis:

mkdir RB_TotalEvidenceDating_FBD_Tutorial

Move to that directory:

cd RB_TotalEvidenceDating_FBD_Tutorial

Get the data files:

wget https://github.com/revbayes/revbayes_tutorial/raw/master/RB_TotalEvidenceDating_FBD_Tutorial/data.zip

Unzip the data folder:

unzip data.zip

Create a directory to hold your RevBayes scripts:

mkdir scripts

Running RevBayes on the MBL Cluster

Execute RevBayes while inside RB_TotalEvidenceDating_FBD_Tutorial:

rb