DomArchov is a novel domain architecture evolution simulator that models the processes of domain gain and loss by which the architectures of multidomain proteins evolve. Although these processes have the potential to generate any combination of domains, only a tiny fraction of possible domain combinations are observed in nature, suggesting that domain order and co-occurrence are stringently constrained. DomArchov is the first simulator to model evolutionary trajectories that reflect the constraints on domain order and co-occurrence observed in nature.

DomArchov models the evolution of domain architectures by combining Markov chain Monte Carlo sampling with data-driven estimates of domain gain and loss probabilities. The use of a data-driven event module enables quick and easy redeployment of the simulator for use in different taxonomic and protein function contexts. Empirical evaluation with metazoan datasets verifies that domain architectures simulated by DomArchov recapitulate properties of genuine domain architectures seen in nature. This work expands the realm of evolutionary processes that are amenable to simulation.

DomArchov is written in python.

Click here to download the DomArchov package.

DomArchov was written by Collin McCormick, Yifan Xue, Xiaoyue Cui, Yangi Yi, Alejandro Garces, and Maureen Stolzer, Dannie Durand and is based on the work described in

Simulating Domain Architecture Evolution.
        X. Cui, Y. Xue, C. McCormack, A. Garces, T.W. Rachman, Y. Yi, M. Stolzer, and D. Durand, Bioinformatics, 2022.
        https://doi.org/10.1093/bioinformatics/btac242.

This work was supported in part by NSF Grant DBI1262593.   Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.