Index of /examples/bioinformatics/beast2

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[DIR] Parent Directory - [   ] GeneralNotes.pdf 18-Nov-2015 09:27 72K [   ] primate-mtDNA.nex 18-Nov-2015 09:35 15K [   ] testRNA.xml 18-Nov-2015 10:14 23K [   ] testRNA.log 18-Nov-2015 10:17 173K [   ] testRNA.trees 18-Nov-2015 10:17 259K [   ] testRNA.xml.state 18-Nov-2015 10:17 3.4K
Index of Beast2

Beast2 Usage and Examples


BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies 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 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results.

Developer Site:

Usage Notes

  1. Load modules:
  2. scc % module load java
    scc % module load beast2

  3. Display Beast2 command usage:
  4. scc % beast -help
    jardir = /share/pkg/beast2/2.3.1/install/beast/lib/launcher.jar
    Checking out /share/pkg/beast2/2.3.1/install/beast/lib
    Loaded URL file:/share/pkg/beast2/2.3.1/install/beast/lib/beast.jar
      Usage: beast [-window] [-options] [-working] [-seed] [-prefix ] [-statefile ] [-overwrite] [-resume] [-errors ] [-threads ] [-java] [-noerr] [-loglevel ] [-beagle] [-beagle_info] [-beagle_order ] [-beagle_instances ] [-beagle_CPU] [-beagle_GPU] [-beagle_SSE] [-beagle_single] [-beagle_double] [-beagle_scaling ] [-help] []
        -window Provide a console window
        -options Display an options dialog
        -working Change working directory to input file's directory
        -seed Specify a random number generator seed
        -prefix Specify a prefix for all output log filenames
        -statefile Specify the filename for storing/restoring the state
        -overwrite Allow overwriting of log files
        -resume Allow appending of log files
        -errors Specify maximum number of numerical errors before stopping
        -threads The number of computational threads to use (default auto)
        -java Use Java only, no native implementations
        -noerr Suppress all output to standard error
        -loglevel error,warning,info,debug,trace
        -beagle Use beagle library if available
        -beagle_info BEAGLE: show information on available resources
        -beagle_order BEAGLE: set order of resource use
        -beagle_instances BEAGLE: divide site patterns amongst instances
        -beagle_CPU BEAGLE: use CPU instance
        -beagle_GPU BEAGLE: use GPU instance if available
        -beagle_SSE BEAGLE: use SSE extensions if available
        -beagle_single BEAGLE: use single precision if available
        -beagle_double BEAGLE: use double precision if available
        -beagle_scaling BEAGLE: specify scaling scheme to use
        -help Print this information and stop
      Example: beast test.xml
      Example: beast -window test.xml
      Example: beast -help

  5. Beast example usage
  6. scc % 
    beast testRNA.xml

Contact Information

RCS Apps Team:

Document written by Katia Oleinik on 11/20/2015. Last modified on 11/20/2015.