rnasim: Simulating RNA evolution

eagle-i ID

Resource Type

Properties

1. Resource Description

   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.

2. Used by

   Kim Laboratory: Computational Evolutionary Biology

3. Version

   1.0

4. Operating System

   Linux

5. Data Input

   Tree file

6. Data Input

   RNA sequence and secondary structure

7. Data Output

   RNA sequences

8. Data Output

   RNA secondary structures

9. Data Output

   Nucleotide positions in the homologous alignment

10. Data Output

    RNA sequence identifier (node name in the tree)

11. Data Output

    Scaled tree used in simulation

12. Software purpose

    Evolutionary modeling objective

13. Related Publication or Documentation

    Large-scale simulation of RNA macroevolution by an energy-dependent fitness model

14. Website(s)

    http://kim.bio.upenn.edu/software/rnasim.shtml

15. Related Technique

    Computational modeling technique

16. Developed by

    Kim, Junhyong, Ph.D.

17. Developed by

    Wang, Li-San, Ph.D.

18. Developed by

    Guo, Sheng

19. Software license

    Academic software license

20. Coded in

    C++