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rnasim: Simulating RNA evolution
eagle-i ID
http://eagle-i.itmat.upenn.edu/i/0000013d-5f9c-2ba8-5757-7bd780000000
Resource Type
Properties
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Resource Description
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Simulated nucleotide sequences are widely used in theoretical and empirical molecular evolution studies. Conventional simulators generally use fixed parameter time-homogeneous Markov model for sequence evolution. rnasim simulates RNA evolution on phylogenies based on the model described in the related publication. Briefly, rnasim uses the folding free energy of the secondary structure of an RNA, the energy_of_struct() class in the Vienna RNA package, as a proxy for its phenotypic fitness, and simulates RNA macroevolution by a mutation-selection population genetics model. Because the two-step process is conditioned on an RNA and its mutant ensemble, we no longer have a global substitution matrix, nor do we explicitly assume any for this inhomogeneous stochastic process. The sequences generated by rnasim, have greater statistical complexity than sequences generated by two standard simulators, ROSE and Seq-Gen, and are close to empirical sequences.
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Used by
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Kim Laboratory: Computational Evolutionary Biology
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Version
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1.0
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Operating System
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Linux
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Data Input
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Tree file
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Data Input
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RNA sequence and secondary structure
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Data Output
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RNA sequences
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Data Output
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RNA secondary structures
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Data Output
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Nucleotide positions in the homologous alignment
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Data Output
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RNA sequence identifier (node name in the tree)
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Data Output
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Scaled tree used in simulation
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Software purpose
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Evolutionary modeling objective
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Related Publication or Documentation
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Large-scale simulation of RNA macroevolution by an energy-dependent fitness model
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Website(s)
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http://kim.bio.upenn.edu/software/rnasim.shtml
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Related Technique
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Computational modeling technique
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Developed by
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Kim, Junhyong., PhD
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Developed by
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Wang, Li-San., PhD
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Developed by
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Guo, Sheng
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Software license
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Academic software license
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Coded in
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C++
