Version

BEAST v1.6.1 is available in Hippu

BEAST v1.6.1 is available in Murska

BEAST v1.6.1 is available in Vuori

Description

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.

Usage

BEAST environment is set up in Hippu, Murska and Vuori with command

module load beast

The component programs can then be started by their name.

To run with the GUI (you will need X server connection):

beauti

beast

beast example.xml

BEAST can be used either interactively with a graphical user interface or in command line mode. Any batch jobs need to be run in the command line mode. Interactive use is best done in Hippu. Longer runs should be done as  batch jobs either in Murska or Vuori. You can of course use the graphical tools in Hippu to set up the run and the do the run itself in Murska or Vuori.

Hippu installation also includes helper programs FigTree and Tracer. They are set up when the BEAST module is loaded and are started with  commands "figtree" and "tracer" respectively. Due to their interactive nature they are not installed on Murska or Vuori, so you should transfer your results to Hippu if you wish to use
these.

You need a X server connection to use the graphical interfaces. If you have trouble setting this up, you might also consider running beauti locally on your own computer and transferring the resulting .xml files to CSC for analysis in command line mode.

beast -beagle_SSE example.xml

beast -beagle_CPU example.xml

#!/bin/csh
# These commands are for the batch job system
#BSUB -e beast_test_err_%J
#BSUB -o beast_test_out_%J
#BSUB -M 1048576
#BSUB -W 2:00
#BSUB -n 1

# BEAST command line
beast  example.xml

The batch job is submitted with command (where "my_job_script" is the name of your batch file):

bsub < my_job_script

To submit a BEAST job in Vuori, you must construct a command file that includes queue options and setup and execution commands for BEAST.

Please note that all your files need to be in the $WRKDIR directory.

You can modify the following example batch file accordingly where necessary.

#!/bin/csh

## name of your job
#SBATCH -J my_jobname

## system error message output file
#SBATCH -e my_output_err_%j

## system message output file
#SBATCH -o my_output_%j

## a per-process (soft) memory limit
## limit is specified in MB
## example: 1 GB is 1000
#SBATCH --mem-per-cpu=1000

## how long a job takes, wallclock time hh:mm:ss
#SBATCH -t 01:01:00

## number of proceses
#SBATCH -n 1

## run my executable
srun beast example.xml

The batch job is submitted with command (where "my_job_script" is the name of your batch file):

sbatch my_job_script