hstrat: a Python Package for phylogenetic inference on distributed digital evolution populations

Digital evolution systems instantiate evolutionary processes over populations of virtual agents in silico. These programs can serve as rich experimental model systems. Insights from digital evolution experiments expand evolutionary theory, and can often directly improve heuristic optimization techniques . Perfect observability, in particular, enables in silico experiments that would be otherwise impossible in vitro or in vivo. Notably, availability of the full evolutionary history (phylogeny) of a given population enables very powerful analyses.

As a slow but highly parallelizable process, digital evolution will benefit greatly by continuing to capitalize on profound advances in parallel and distributed computing, particularly emerging unconventional computing architectures. However, scaling up digital evolution presents many challenges. Among these is the existing centralized perfect-tracking phylogenetic data collection model, which is inefficient and difficult to realize in parallel and distributed contexts. Here, we implement an alternative approach to tracking phylogenies across vast and potentially unreliable hardware networks.

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Moreno M.A., Dolson, E., & Ofria, C. (2022). hstrat: a Python Package for phylogenetic inference on distributed digital evolution populations. Journal of Open Source Software, 7(80), 4866, https://doi.org/10.21105/joss.04866

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