BEAST v2.0 ReadMe File — this site is deprecated: goto https://www.beast2.org/ for up-to-date information

BEAST v2.0 ReadMe File

                    BEAST v2.0.c 2011

                 Beast 2 development team 2011



Last updated: 1st December 2011



Contents:

1) INTRODUCTION

2) INSTALLING BEAST

3) CONVERTING SEQUENCES

4) RUNNING BEAST

5) ANALYZING RESULTS

6) NATIVE LIBRARIES

7) SUPPORT & LINKS

8) ACKNOWLEDGMENTS 



___________________________________________________________________________

1) INTRODUCTION



BEAST (Bayesian evolutionary analysis sampling trees) is package for

evolutionary inference from molecular sequences.



BEAST uses a complex and powerful input format (specified in XML) to

describe the evolutionary model. This has advantages in terms of

flexibility in that the developers of BEAST do not have to try and predict

every analysis that researchers may wish to perform and explicitly provide

an option for doing it. However, this flexibility means it is possible to

construct models that don't perform well under the Markov chain Monte Carlo

(MCMC) inference framework used. We cannot test every possible model that

can be used in BEAST. There are two solutions to this: Firstly, we  supply

a range of recipes for commonly performed analyses that we know should work

in BEAST and provide example input files for these (although, the actual

data can also produce unexpected behavour). Secondly, we provide advice and

tools for the diagnosis of problems and suggestions on how to fix them:



<http://beast2.cs.auckland.ac.nz/>



BEAST is not a black-box into which you can put your data and expect an

easily interpretable answer. It requires careful inspection of the output

to check that it has performed correctly and usually will need tweaking,

adjustment and a number of runs to get a valid answer. Sorry.



___________________________________________________________________________

2) INSTALLING BEAST



BEAST requires a Java Virtual Machine to run. Many systems will already

have this installed. It requires at least version 1.6 of Java to run. The

latest versions of Java can be downloaded from:



<http://java.sun.com/>



If in doubt type "java -version" to see what version of java is installed

(or if it is installed at all).



Mac OS X will already have a suitable version of Java installed.



Within the BEAST package will be the following directories:

Directory       Contents

doc/            Documentation of BEAST

examples/       Some NEXUS and XML files

lib/            Java & native libraries used by BEAST 

bin/            Scripts of the corresponding OS

templates/      Templates to initiate BEAUti



___________________________________________________________________________

3) CONVERTING SEQUENCES



A program called "BEAUti" will import data in NEXUS format, allow you to

select various models and options and generate an XML file ready for use in

BEAST.



To run BEAUti simply double-click the "BEAUti.exe" file in the BEAST

folder. If this doesn't work then you may not have Java installed correctly. 

Try opening an MS-DOS window and typing:



	java -cp lib/beast.jar beast.app.beauti.Beauti



__________________________________________________________________________

4) RUNNING BEAST



To run BEAST simply double-click the "BEAST.exe" file in the BEAST

folder. You will be asked to select a BEAST XML input file.



Alternatively open a Command window and type:

	

	java -jar lib/beast.jar input.xml



Where "input.xml" is the name of a BEAST XML format file. This file can

either be created from scratch using a text editor or be created by the

BEAUti program from a NEXUS format file. 



For documentation on creating and tuning the input files look at the

documentation and tutorials on-line at:



Help -      <http://beast2.cs.auckland.ac.nz/>

FAQ -       <http://beast2.cs.auckland.ac.nz/index.php/FAQ>

Tutorials - <http://beast2.cs.auckland.ac.nz/index.php/Main_Page#BEAST_2_Tutorials>



BEAST arguments:

     -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"

     -overwrite      "Allow overwriting 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"

     -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"

     

For example:



     java -jar lib/beast.jar -seed 123456 -overwrite input.xml



___________________________________________________________________________

5) ANALYZING RESULTS



We have produced a powerful graphical program for analysing MCMC log files

(it can also analyse output from MrBayes and other MCMCs). This is called

'Tracer' and is available from the Tracer web site:



<http://tree.bio.ed.ac.uk/software/tracer>



Additionally, two new programs are distributed as part of the BEAST

package: LogCombiner & TreeAnnotator. LogCombiner can combine log or tree

files from multiple runs of BEAST into a single combined results file

(after removing appropriate burn-ins). TreeAnnotator can summarize a sample

of trees from BEAST using a single target tree, annotating it with

posterior probabilities, HPD node heights and rates. This tree can then be

viewed in a new program called 'FigTree' which is available from:



<http://tree.bio.ed.ac.uk/software/figtree>



or 'DensiTree' available from BEAST package.



___________________________________________________________________________

6) NATIVE LIBRARIES



May add in the future.



___________________________________________________________________________

7) SUPPORT & LINKS



BEAST is an extremely complex program and as such will inevitably have

bugs. Please email us to discuss any problems:



<remco@cs.auckland.ac.nz>

<alexei@cs.auckland.ac.nz>

<a.rambaut@ed.ac.uk>

<msuchard@ucla.edu>



The BEAST users' mailing-list is coming soon.



The website for beast is here:



<http://beast2.cs.auckland.ac.nz/>



Source code distributed under the GNU Lesser General Public License:



<http://code.google.com/p/beast2/>



___________________________________________________________________________

8) SDK FOR PLUGIN DEVELOPERS



Beast.II.Getting.Started.pdf: Contains description and hints on how to get started with the SDK



LICENSE: LGPL 



beast.jar: Beast 2 library



javadoc/: class documentation



___________________________________________________________________________

9) ACKNOWLEDGMENTS



Thanks for supplying code or assisting with the creation

or testing of Beast 2 development team.






 

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