V ai Phy: a Variational Inference Based Algorithm for Phylogeny Appendix A The V aiPhy Algorithm

The update equations of V aiPhy follow the standard mean-field VI updates. Furthermore, i is the set of nodes except node i, and C is a constant. We utilize the NJ algorithm to initialize V aiPhy with a reasonable state. An example script to run PhyML is shown below. Here we provide two algorithmic descriptions of SLANTIS.