Brief Reports
Vol. 4 No. 1 (2012)
https://doi.org/10.4081/eb.2012.e9

CASS: Protein sequence simulation with explicit genotype-phenotype mapping

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Received: 13 July 2012
Accepted: 8 October 2012
Published: 13 November 2012
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sequence-structure-function relationship, simulation, molecular evolution

Authors

Johan A. Grahnen
Department of Molecular Biology, University of Wyoming, Laramie, WY, United States.
David A. Liberles
liberles@uwyo.edu
Department of Molecular Biology, University of Wyoming, Laramie, WY, United States.
CASS (coarse-grained artificial sequence simulator) is a software package for simulating protein sequences with an explicit genotype-to-phenotype mapping that takes protein structure and function into account. It is capable of reproducing many structure-specific properties of protein sequence evolution, most notably spatial and temporal variation in rates, and has been used to investigate several hypotheses about the influence of thermodynamics on molecular evolution. The software is implemented in object-oriented C++, is supported on Linux, and the source code is made freely available under the GPL v3 license at http://www.wyomingbioinformatics.org/Liberle sGroup/CASS/.

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CASS: Protein sequence simulation with explicit genotype-phenotype mapping. (2012). Trends in Evolutionary Biology, 4(1), e9. https://doi.org/10.4081/eb.2012.e9