Commit a64c706d authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.1.2+git20180619

parent e4b0fabf

.travis.yml

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@@ -44,10 +44,19 @@ install: 
before_script:

 - ulimit -c unlimited -S # Enable core dumps



after_failure:

 - cat /home/travis/build/beagle-dev/beagle-lib/examples/synthetictest/test-suite.log

 - cat /home/travis/build/beagle-dev/beagle-lib/examples/tinytest/test-suite.log

 - cat /home/travis/build/beagle-dev/beagle-lib/examples/oddstatetest/test-suite.log

 - cat /home/travis/build/beagle-dev/beagle-lib/examples/complextest/test-suite.log

 - cat /home/travis/build/beagle-dev/beagle-lib/examples/fourtaxon/test-suite.log

 - cat /home/travis/build/beagle-dev/beagle-lib/examples/matrixtest/test-suite.log 



# Build steps

script:

  - ./autogen.sh

  - ./configure  --with-opencl=${AMDAPPSDKROOT}

#  - ./configure  --with-opencl=${AMDAPPSDKROOT}

  - ./configure  --without-opencl

  - make

  - make check

AUTHORS

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The BEAGLE Developer group (http://beagle-lib.googlecode.com)
 
The BEAGLE Developer group (https://github.com/beagle-dev)

Makefile.am

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@@ -13,7 +13,7 @@ java/beagle/GeneralBeagleImpl.java \ 
project/beagle-xcode/beagle-xcode.xcodeproj/project.pbxproj \

project/beagle-vs/complextest/complextest_vc90.vcproj \

project/beagle-vs/fourtaxon/fourtaxon_vc90.vcproj \

project/beagle-vs/genomictest/genomictest_vc90.vcproj \

project/beagle-vs/synthetictest/synthetictest_vc90.vcproj \

project/beagle-vs/tinytest/tinytest_vc90.vcproj \

project/beagle-vs/oddstatetest/oddstatetest_vc90.vcproj \

project/beagle-vs/matrixtest/matrixtest_vc90.vcproj \
@@ -51,7 +51,7 @@ OPTIMIZATIONS= -O3 -mfpmath=sse -ftree-vectorizer-verbose=5 -msse -msse2 -ffast- 
profile:

	make clean

	make CXXFLAGS="$(CXXFLAGS) -fprofile-generate $(OPTIMIZATIONS)"

	make -C examples/genomictest/ check CXXFLAGS="$(CXXFLAGS) -static -fprofile-generate $(OPTIMIZATIONS)"

	make -C examples/synthetictest/ check CXXFLAGS="$(CXXFLAGS) -static -fprofile-generate $(OPTIMIZATIONS)"

	make mostlyclean

	make CXXFLAGS="$(CXXFLAGS) -fprofile-use $(OPTIMIZATIONS)"

README

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# @author Marc A. Suchard

# @author Andrew Rambaut



This is a stem README file.   This file will contain:

# @author Daniel L. Ayres



1. General overview of BEAGLE



BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian

and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those

in graphics cards (GPUs) found in many PCs.



The project involves an open API and fast implementations of a library for evaluating phylogenetic

likelihoods (continuous time Markov processes) of biomolecular sequence evolution.



The aim is to provide high performance evaluation ‘services’ to a wide range of phylogenetic software,

both Bayesian samplers and Maximum Likelihood optimizers. This allows these packages to make use of

implementations that make use of optimized hardware such as graphics processing units.



2. Compilation instructions



Quick and dirty instructions on how to compile and install the BEAGLE library from the SVN repository 'trunk':

Quick and dirty instructions on how to compile and install the BEAGLE library from the git repository 'master':



      $ svn checkout http://beagle-lib.googlecode.com/svn/trunk BEAGLE

      $ cd BEAGLE

      $ git clone --depth=1 https://github.com/beagle-dev/beagle-lib.git

      $ cd beagle-lib

      $ ./autogen.sh

      $ ./configure

      $ make
@@ -19,17 +29,15 @@ Quick and dirty instructions on how to compile and install the BEAGLE library fr 
Remarks:



When compiling in the MacOS Unix environment ("Terminal"), you need to install the autotools first. They are no

longer shipped with Xcode. For instance, you can install them using MacPorts (http://www.macports.org). First

install MacPorts, then do:



      $ sudo port install autoconf

      $ sudo port install automake

      $ sudo port install libtool

      $ sudo port install pkgconfig

longer shipped with Xcode. you need to obtain the following software packages: autoconf, automake, and libtool.

The easiest way to install these is with the Homebrew package manager (http://brew.sh/). Open 'Terminal.app'

and paste the installation command from the Homebrew website (you will find it at the top of the page, under

Install Homebrew). Next enter the following to install the required packages:



The last tool is not needed by BEAGLE but by many other software packages. Other options to install autotools

include Homebrew (http://mxcl.github.io/homebrew/) and directly from GNU source (http://www.gnu.org).

      $ brew install libtool autoconf automake



3. Contact information



BEAGLE developer group: beagle-dev@googlegroups.com

README.md

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### Overview



BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs.



The project involves an open API and fast implementations of a library for evaluating phylogenetic likelihoods (continuous time Markov processes) of biomolecular sequence evolution.
@@ -5,29 +7,37 @@ The project involves an open API and fast implementations of a library for evalu 
The aim is to provide high performance evaluation 'services' to a wide range of phylogenetic software, both Bayesian samplers and Maximum Likelihood optimizers. This allows these packages to make use of implementations that make use of optimized hardware such as graphics processing units.



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

- BEAST http://beast.bio.ed.ac.uk/

- Garli https://garli.googlecode.com/

- MrBayes http://mrbayes.sourceforge.net/

- PhyML https://phyml.googlecode.com/



A manuscript describes the BEAGLE API and library:  

http://sysbio.oxfordjournals.org/content/61/1/170

* 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/)



### References



A manuscript describes the BEAGLE API and library:  [http://sysbio.oxfordjournals.org/content/61/1/170](http://sysbio.oxfordjournals.org/content/61/1/170)



The paper describing the algorithms used for calculating likelihoods of sequences on trees using many core devices like graphics processing units (GPUs) is available from:  [http://tree.bio.ed.ac.uk/publications/390/](http://tree.bio.ed.ac.uk/publications/390/)



The paper describing the algorithms used for calculating likelihoods of sequences on trees using many core devices like graphics processing units (GPUs) is available from:  

http://tree.bio.ed.ac.uk/publications/390/  

### 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)



Binary installers:

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

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



### Installation instructions



* [Instructions for installing BEAGLE on macOS](https://github.com/beagle-dev/beagle-lib/wiki/MacInstallInstructions)

* [Instructions for installing BEAGLE on Windows](https://github.com/beagle-dev/beagle-lib/wiki/WindowsInstallInstructions)

* [Instructions for installing BEAGLE on Linux](https://github.com/beagle-dev/beagle-lib/wiki/LinuxInstallInstructions) 



### Documentation



Installation instructions:

- [Instructions for installing BEAGLE on Mac OS X](https://github.com/beagle-dev/beagle-lib/wiki/MacInstallInstructions)

- [Instructions for installing BEAGLE on Windows](https://github.com/beagle-dev/beagle-lib/wiki/WindowsInstallInstructions)

- [Instructions for installing BEAGLE on Linux](https://github.com/beagle-dev/beagle-lib/wiki/LinuxInstallInstructions) 

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

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



Documentation:

- [API documentation](http://beagle-lib.googlecode.com/svn/doc/html/beagle_8h.html)

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

### Acknowledgements



# Acknowledgements

- This project is supported in part through the National Science Foundation grants IIS 1251151 and DMS 1264153.
 
* This project is supported in part through the National Science Foundation grants IIS-1251151, DMS-1264153, DBI-1356562, DBI-1661443, & DEB-1354146; National Institutes of Health grants R01-HG006139, R01-AI107034, & U19-AI135995; Wellcome Trust grant 206298/Z/17/Z; and European Research Council grant 725422-ReservoirDOCS.