CASS: Protein sequence simulation with explicit genotype-phenotype mapping


https://doi.org/10.4081/eb.2012.e9
Vol. 4 No. 1 (2012)
Submitted: 13 July 2012
Accepted: 8 October 2012
Published: 13 November 2012
sequence-structure-function relationship, simulation, molecular evolution
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Authors

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/.

Supporting Agencies


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

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