phastSim (fast phylogenetic simulator) describes a new algorithm and software for simulating sequence evolution along large trees when the branches of the tree are short, as is typical in genomic epidemiology. The algorithm is based on the Gillespie approach and implements an efficient multi-layered search tree structure that provides high computational efficiency. The software allows easy integration with other Python packages as well as a variety of evolutionary models, including indel models and new hypermutability models that were developed to more realistically represent SARS-CoV-2 genome evolution.

For details see the paper:

https://doi.org/10.1371/journal.pcbi.1010056