Commit 2d02d401 authored by Andreas Tille's avatar Andreas Tille
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New upstream version 3.1.2+dfsg

parent 16f18654

README.md

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Currently the following software packages can make use of the BEAGLE library:



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

* Garli [https://molevol.mbl.edu/index.php/Garli_wiki](https://molevol.mbl.edu/index.php/Garli_wiki)

* MrBayes [http://mrbayes.sourceforge.net/](http://mrbayes.sourceforge.net/)

* PhyML [http://www.atgc-montpellier.fr/phyml/](http://www.atgc-montpellier.fr/phyml/)

* [BEAST](http://beast.community/)

* [BEAST2](http://beast2.org/)

* [MrBayes](https://github.com/NBISweden/MrBayes)



Support for BEAGLE is experimental or in development for the following packages:



* [Garli](https://molevol.mbl.edu/index.php/Garli_wiki)

* [PhyML](http://www.atgc-montpellier.fr/phyml/)

* [RevBayes](https://revbayes.github.io)

* [PAUP*](https://paup.phylosolutions.com)



### References
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### Binary installers



* [BEAGLE v3.0.2 for macOS](https://github.com/beagle-dev/beagle-lib/releases/download/v3.0.2/BEAGLE.v3.0.2.pkg)

* [BEAGLE v3.0.1 for Windows 64-bit](https://github.com/beagle-dev/beagle-lib/releases/download/v3.0.1/BEAGLE.v3.0.1.msi)

* [BEAGLE v3.1.0 for macOS](https://github.com/beagle-dev/beagle-lib/releases/download/v3.1.0/BEAGLE.v3.1.0.pkg)

* [BEAGLE v3.1.0 for Windows 64-bit](https://github.com/beagle-dev/beagle-lib/releases/download/v3.1.0/BEAGLE.v3.1.0.msi)



- [BEAGLE v2.1.2 for Mac OS X 10.6 and later](https://www.dropbox.com/s/11kgt2jlq3lzln3/BEAGLE-2.1.2.pkg)

- [BEAGLE v2.1.0 for Windows XP and later](https://www.dropbox.com/s/61z48jvruzkwkku/BEAGLE-2.1.msi)
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### Documentation



* [API documentation](https://beagle-dev.github.io/html/beagle_8h.html)

* [Release notes](https://github.com/beagle-dev/beagle-lib/wiki/ReleaseNotes)

* [API documentation](https://beagle-dev.github.io/html/beagle_8h.html)

* [Phylogenetic Software Development Tutorial](https://phylogeny.uconn.edu/tutorial-v2/)



### Acknowledgements

app-benchmarks/v3-app-note/Dengue997_s3_AMVN_BTL.xml→benchmarks/v3-app-note/Dengue997_s3_AMVN_BTL.xml

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	</operators>









	<!-- Define MCMC                                                             -->









	<mcmc id="mcmc" chainLength="1000" autoOptimize="true" operatorAnalysis="Dengue997_s3.ops">









	<mcmc id="mcmc" chainLength="100000" autoOptimize="true" operatorAnalysis="Dengue997_s3.ops">









		<posterior id="posterior">









			<prior id="prior">









				<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">

























app-benchmarks/v3-app-note/Dengue997_s3_AMVN_MPDLD.xml→benchmarks/v3-app-note/Dengue997_s3_AMVN_MPDLD.xml



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	</operators>

















	<!-- Define MCMC                                                             -->









	<mcmc id="mcmc" chainLength="1000" autoOptimize="true" operatorAnalysis="Dengue997_s3.ops">









	<mcmc id="mcmc" chainLength="100000" autoOptimize="true" operatorAnalysis="Dengue997_s3.ops">









		<posterior id="posterior">









			<prior id="prior">









				<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">

























benchmarks/v3-app-note/Dengue997_s3_codon.xml
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