Supporting information for: Lagrange-NG: The Next Generation of Lagrange

Computing ancestral ranges via the Dispersion Extinction and Cladogensis
(DEC) model of biogeography is characterized by an exponential number of
states relative to the number of regions considered. This is because the
DEC model requires computing a large matrix exponential, which typically
accounts for up to 80% of overall runtime. Therefore, the kinds of
biogeographical analyses that can be conducted under the DEC model are
limited by the number of regions under consideration. In this work, we
present a completely redesigned efficient version of the popular tool
Lagrange which is up to 2.5 times faster, which we call Lagrange-NG (Next
Generation). We further reduce time-to-completion by introducing a
multi-grained parallelization approach, achieving a total parallel speedup
of 8.5 over Lagrange on a machine with 8 cores. In order to validate the
correctness of Lagrange-NG, we also introduce a novel metric on range
distributions for trees in order to assess the difference between any two
range inferences. Finally, Lagrange-NG exhibits substantially higher
adherence to coding quality standards. It improves a respective software
quality indicator as implemented in the SoftWipe tool from average (5.5;
Lagrange) to high (7.8; Lagrange-NG). Lagrange-NG is freely available
under GPL2.