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:

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:


Installing BEAST

Installing BEAST on Linux

To add:

  • Unpacking tarball.
  • Moving directory to /usr/local/ or some such place.
  • Describing the shell scripts in /bin.
  • Creating symbolic links?
  • Running directly using the .jar file (to allow JavaVM options).
  • Running without command-line options to bring up GUI.