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: <email@example.com> <firstname.lastname@example.org> <email@example.com> <firstname.lastname@example.org> 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.