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SodaPop: A computational suite for simulating the dynamics of asexual populations

View ORCID ProfileLouis Gauthier, Remicia Di Franco, View ORCID ProfileAdrian Serohijos
doi: https://doi.org/10.1101/189142
Louis Gauthier
University of Montreal
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Remicia Di Franco
University of Montreal
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Adrian Serohijos
University of Montreal
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  • For correspondence: adrian.serohijos@umontreal.ca
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Abstract

Motivation: Simulating protein evolution with realistic constraints from population genetics is essential in addressing problems in molecular evolution, from understanding the forces shaping the evolutionary landscape to the clinical challenges of antibiotic resistance, viral evolution and cancer. Results: To address this need, we present SodaPop, a new forward-time simulator of large asexual populations aimed at studying their structure, dynamics and the distribution of fitness effects with flexible assumptions on the fitness landscape. SodaPop integrates biochemical and biophysical properties in a cell-based, object-oriented framework and provides an efficient, open-source toolkit for performing large-scale simulations of protein evolution. Availability and implementation: Source code and binaries are freely available at https://github.com/louisgt/SodaPop under the GNU GPLv3 license. The software is implemented in C++ and supported on Linux, Mac OS/X and Windows.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted September 15, 2017.
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SodaPop: A computational suite for simulating the dynamics of asexual populations
Louis Gauthier, Remicia Di Franco, Adrian Serohijos
bioRxiv 189142; doi: https://doi.org/10.1101/189142
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SodaPop: A computational suite for simulating the dynamics of asexual populations
Louis Gauthier, Remicia Di Franco, Adrian Serohijos
bioRxiv 189142; doi: https://doi.org/10.1101/189142

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