Implementing Bayesian phylogenetic tree inference with Sequential Monte Carlo and the Phylogenetic Likelihood Library
Isaac Arvestad, Henrik Lagebrand · KTH Publication Database DiVA (KTH Royal Institute of Technology) · 2018
We investigate the usability of the Phylogenetic Likelihood Library (PLL) in Bayesian phylogenetic tree inference using Sequential Monte Carlo (SMC) algorithms. This is done by implementing two different versions of the same algorithm with two different approaches of the use of PLL. The implementation using the main PLL API encountered performance issues that the lower level implementation did not. We conclude that it is possible to use PLL in SMC methods but it is unclear if the main API is suitable.