How to install BEAST2 on our linux server

Version 0.2

You need to install a copy of BEAST (here version 2.6.4) into your local folder to run it on the server: The location for finding the latest version is at https://github.com/CompEvol/beast2/releases

cd ~
mkdir -p /programs
cd programs
wget https://github.com/CompEvol/beast2/releases/download/v2.6.4/BEAST.v2.6.4.Linux.tgz
tar zxvf BEAST.v2.6.4.Linux.tgz

To start BEAST:

~/programs/beast/bin/beast yourinputfile.xml

or

java -jar ~/programs/beast/lib/launcher.jar input.xml -help

for more information.

To start BEAST with multiple cores (here use 4) type:

~/programs/beast/bin/beast -threads 4 yourinputfile.xml

To install the BEAGLE library for high performance evaluation in BEAST, type:

conda install -c bioconda beagle-lib

and then to use beagle library if available type:

java -jar ~/programs/beast/lib/launcher.jar -beagle input.xml

to use use SSE extensions if available type:

java -jar ~/programs/beast/lib/launcher.jar -beagle_SSE input.xml