BEAST is a software package for phylogenetic analysis with an emphasis on time-scaled trees.

Downloading BEAST

BEAST can be downloaded from the following link:

This will download a compressed tar archive (a ‘.tgz’ file).

The latest version of BEAST can always be found here: https://github.com/beast-dev/beast-mcmc/releases/latest

Installing JAVA

Installing OpenJDK 8

Ubuntu-based linux operating systems have Open JDK installed as their default Java installation. To install Open JDK 8 (both JRE and JDK), you can run the following commands:

sudo apt-get install openjdk-8-jre
sudo apt-get install openjdk-8-jdk

Installing Oracle Java 8

If you’d like to use Oracle Java instead of Open JDK, you will require the PPA maintained by Webupd8 Team before proceeding with the installation:

sudo apt-add-repository ppa:webupd8team/java
sudo apt-get update
sudo apt-get install oracle-java8-installer

Note: if the apt-add-repository command is not found, first install the following:

sudo apt-get install software-properties-common

The PPA also contains a package to automatically set Java environment variables, by simply running the following command:

sudo apt-get install oracle-java8-set-default

You can now edit the /etc/environment configuration file and add the following entries to set JAVA_HOME and JRE_HOME environment variables:

JAVA_HOME=/usr/lib/jvm/java-8-oracle
JRE_HOME=/usr/lib/jvm/java-8-oracle/jre

Installing BEAST

Downloading and running BEAST on Linux

Start by downloading and unpacking the compressed .tar.gz file:

tar -zxvf BEASTv1.10.4.tgz

You can now go to the /bin directory and run BEAUti and BEAST from this directory:

cd BEASTv1.10.4/bin
./beauti
./beast

Adding the executables to the system path

To add the BEAUti and BEAST executables to the system’s path (to run from outside the /bin directory), you need to edit your system’s profile:

nano ~/.bash_profile

and add the path to the /bin directory:

export PATH=$PATH:$HOME/BEASTv1.10.4/bin/

To reload the changes to the profile immediately without logging out or restarting your computer, run the following:

source ~/.bash_profile

Verify your current system’s path settings by typing:

echo $PATH

ln -s Downloads/BEASTv1.10.4/bin/beauti beauti
ln -s Downloads/BEASTv1.10.4/bin/beast beast

Running BEAST from a jar file (with GUI)

Go to the /lib directory where you extracted the linux .tar.gz file:

cd BEASTv1.10.4/lib
java -jar beauti.jar
java -jar beast.jar

Running BEAUti and BEAST from a jar file (without GUI)

In that same /lib directory, provide command-line options for BEAST to run with:

java -jar beast.jar -seed 1234 example.xml
Tags: