What is BEAGLE and should I use it? 

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 3D graphics boards (referred to as Graphics Processing Units or GPUs) found in many PCs. In general using it (even if not using a GPU) will improve the performance of BEAST. However, installing it for BEAST to use is not a simple operation  and it is not necessarily going to benefit all data sets. In particular, for the use of a GPU (and currently only NVidia ones are supported) to be efficient, long partitions are required (perhaps >500 unique site patterns). Only high-end GPUs such as the GTX285 or Tesla boards will provide sufficient benefits.

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Bayesian evolutionary analysis by sampling trees