BEAGLE 5.2 – Genetic Analysis Software Package

BEAGLE 5.2

:: DESCRIPTION

BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can

phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios.
infer sporadic missing genotype data.
impute ungenotyped markers that have been genotyped in a reference panel.
perform single marker and haplotypic association analysis.
detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals.

::DEVELOPER

Brian L. Browning

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

BEAGLE

:: MORE INFORMATION

Citation:

B L Browning and S R Browning (2013)
Improving the accuracy and efficiency of identity by descent detection in population data.
Genetics 194(2):459-71. doi:10.1534/genetics.113.150029

B L Browning and S R Browning (2011)
A fast, powerful method for detecting identity by descent.
The American Journal of Human Genetics 88:173-182.

πBUSS 1.4 – BEAST/BEAGLE utility for Sequence Simulation

πBUSS 1.4

:: DESCRIPTION

πBUSS is a BEAST/BEAGLE utility for sequence simulation, which provides an easy to use interface that allows flexible and extensible phylogenetic data fabrication, delegating computationally intensive tasks to the BEAGLE library and thus making full use of multi-core architectures.

::DEVELOPER

Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research

:: SCREENSHOTS

:: REQUIREMENTS

Linux / WIndows / MacOsX
Java

:: DOWNLOAD

πBUSS

:: MORE INFORMATION

Citation

Bielejec, F., Lemey, P., Carvalho, L. M., Baele, G., Rambaut, A., Suchard, M. A. (2014)
πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios.
BMC Bioinformatics 15:133.

BEAGLE 3.1.2 – Evaluating the Likelihood of Sequence Evolution on Trees

BEAGLE 3.1.2

:: DESCRIPTION

BEAGLE-lib (Broad-platform Evolutionary Analysis General Likelihood Evaluator) is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.

::DEVELOPER

BEAGLE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX

:: DOWNLOAD

BEAGLE

:: MORE INFORMATION

Citation

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics.
Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA.
Syst Biol. 2019 Nov 1;68(6):1052-1061. doi: 10.1093/sysbio/syz020.

Syst Biol. 2012 Jan;61(1):170-3. doi: 10.1093/sysbio/syr100.
BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.
Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP, Rambaut A, Suchard MA.