Data from: The phylogenetic likelihood library

We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized
application programming interface for developing likelihood-based
phylogenetic inference and post-analysis software. The PLL implements
appropriate data structures and functions that allow users to quickly
implement common, error-prone, and labor-intensive tasks, such as
likelihood calculations, model parameter as well as branch length
optimization, and tree space exploration. The highly optimized and
parallelized implementation of the phylogenetic likelihood function and a
thorough documentation provide a framework for rapid development of
scalable parallel phylogenetic software. By example of two
likelihood-based phylogenetic codes we show that the PLL improves the
sequential performance of current software by a factor of two to ten while
requiring only one month of programming time for integration. We show
that, when numerical scaling for preventing floating point underflow is
enabled, the double precision likelihood calculations in the PLL are up to
1.9 times faster than those in BEAGLE. On an empirical DNA dataset with
2,000 taxa the AVX version of PLL is 4 times faster than BEAGLE (scaling
enabled and required). The PLL is available at http://www.libpll.org under
the GNU General Public License (GPL).