BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics package. It can make use of highly-parallel processors such as those in graphics processing units (GPUs) found in many PCs.
Using BEAGLE with BEAST
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The current version of BEAGLE will only work with BEAST v1.6 or later
Downloading and installing BEAGLE
https://newgr452.weebly.com/blog/mac-os-mojave-download-space. BEAGLE is an independent project and its website is https://github.com/beagle-dev/beagle-lib, where binary installers and installation instructions for different operating systems are available.
Testing the BEAGLE installation
To test the installation, run BEAST and when the options dialog box appears, select “Use BEAGLE library” and “Show list of available BEAGLE resources”:
You don’t need to specify a BEAST input file as the information about BEAGLE will be displayed and then BEAST will stop. For the commandline version of BEAST, type:
When run, it should show a list of available resources that BEAGLE has detected:
This shows the CPU (which should always be available), an Intel integrated graphics processor (this is the graphics chip that is used to run the computer display) and one NVidia Tesla GPU card specifically designed for scientific computing.
Running BEAST with BEAGLE
You are now ready to run BEAST using BEAGLE. Just run BEAST again and select “Use BEAGLE library” but not the “Show list of available BEAGLE resources” option. When running, as part of the initial pre-amble text, BEAGLE will say what resource it is using:
This shows that BEAGLE will be using the primary CPU and gives some details about the options it will be using. Batim chapter 2 download mac. Close combat 3 mac download. The default options will be optimal for most machines but see this page for information about optimizing BEAST computational performance.
Running BEAST/BEAGLE on command line
Doom 1 download mac free. If you are running BEAST on Linux or wish to have more control of the BEAGLE performance options on Mac OS X or Windows you will need to run BEAST from the command line.
Running BEAST from the command line allows you to select which resource needs to be used for your analysis by using a command-line option.For example, in order to ensure that resource 1 (see above) will be used when running BEAST, you can use the following command:
The full list of command-line BEAGLE options can be listed using
beast -help and are listed here:
Frequently Asked Questions
Citing BEAGLE
A manuscript describes the BEAGLE API and library: 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: https://academic.oup.com/bioinformatics/article/25/11/1370/332982
ContentsIntroduction
Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Beagle 5.1 is similar to version 5.0, but includes some additional improvements that increase accuracy and reduce computation time.
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Citation![]()
If you use Beagle in a published analysis, please report the program version and cite the appropriate article.
The Beagle 5.1 genotype imputation method is described in:
B L Browning, Y Zhou, and S R Browning (2018). A one-penny imputed genome from next generation reference panels. Am J Hum Genet 103(3):338-348. doi:10.1016/j.ajhg.2018.07.015
The most recent reference for Beagle's phasing method is:
S R Browning and B L Browning (2007) Rapid and accurate haplotype phasing and missing data inference for whole genome association studies by use of localized haplotype clustering. Am J Hum Genet 81:1084-1097. doi:10.1086/521987
This reference will be updated when the Beagle version 5 phasing method is published.
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Download Beagle 5.1
Beagle is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
Beagle is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You can download a copy of the the GNU General Public License from http://www.gnu.org/licenses/.
Source files in the net/sf/samtools/ directory are from the Broad Institute and are used to perform BGZIP compression and decompression. Source files from the Broad Institute are licensed under the MIT license.
The following resources are also available:
Download Beagle 4.0
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Download Beagle 4.0 Machine
Copyright: 2013-2020 Brian L. Browning
Last updated: May 18, 2020 Download .NET Framework 4.0 | Free Official DownloadsComments are closed.
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