Researchers at the University of Maryland have developed BEAGLE, an application programming interface and specialized library for high-performance statistical phylogenetic inference that allows existing software packages to make more effective use of available computer hardware including GPUs, CPUs with Streaming SIMD Extensions, and multi-core CPUs via OpenMP.
The team profiled their research in Systematic Biology and write that "a specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future."
BEAGLE is compatible with Mac, Windows, and Linux operating systems. It is freely available for download here.