Commit 019d7333 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.10.0+dfsg

parent c43ea5aa

.gitignore

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build/

dist/

out/

.idea

.idea/libraries/lib.xml

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<component name="libraryTable">

  <library name="lib">

    <CLASSES>

      <root url="file://$PROJECT_DIR$/lib" />

    </CLASSES>

    <JAVADOC />

    <SOURCES />

    <jarDirectory url="file://$PROJECT_DIR$/lib" recursive="false" />

  </library>

</component>
 
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.idea/uiDesigner.xml

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</project>
 
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.travis.yml

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language: java

sudo: false



jdk:

    - oraclejdk7

    - openjdk6

#jdk:

#    - oraclejdk7

#    - oraclejdk8

#    - openjdk6



#addons:

#  apt:

#    packages:

#    - ant-junit



script: ant dist

README.md

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# BEAST



Bayesian Evolutionary Analysis Sampling Trees (BEAST) is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. 

The program is orientated towards (strict and relaxed) molecular clock analyses. 

It can be used as a method of constructing phylogenies, but it is also intended 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. 

It uses an XML input format that allows the user to design and run a large range of models. 

We also include a program that can convert NEXUS files into this format.

BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. 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. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.



## Download BEAST



[Download BEAST v1.8.3 binaries for Mac, Windows and UNIX/Linux](http://tree.bio.ed.ac.uk/software/beast/)

[Download BEAST v1.10.0 binaries for Mac, Windows and UNIX/Linux](https://github.com/beast-dev/beast-mcmc/releases/tag/v1.10.0)



[The previous major release of BEAST was v1.8.4 --- binaries for Mac, Windows and UNIX/Linux](https://github.com/beast-dev/beast-mcmc/releases/tag/v1.8.4)



[Older BEAST Downloads](https://code.google.com/p/beast-mcmc/downloads)
@@ -21,14 +18,12 @@ We also include a program that can convert NEXUS files into this format. 


# Documentation



[BEAST Documentation Website](http://beast.bio.ed.ac.uk)

[BEAST Documentation Website](http://beast.community)





# Acknowledgements

- This project is supported in part through the National Science Foundation grant DMS 1264153.

- This work was supported in part by the European Union Seventh Framework Programme for research, technological development and demonstration under Grant Agreement no. 278433-PREDEMICS and no. 725422-ReservoirDOCS, the Wellcome Trust through collaborator award 206298/Z/17/Z, NSF grant DMS 1264153 and NIH grants R01 HG006139, R01 AI107034 and U19 AI135995.



---



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