For mutiple time-point whole-genome NGS experimental evolution data
* Time-serial mutation rate analysis
* Time-serial effective population size analysis
* Time-serial selection analysis
H. Shim. Feature learning of virus genome evolution with the nucleotide skip-gram neural networks (accepted in NIPS 2017 Workshop).
A. Carratalà, H. Shim, Q. Zhong, V. Bachmann, J.D. Jensen, T. Kohn. Experimental adaptation of human echovirus 11 to ultraviolet radiation leads to tolerance to disinfection and resistance to ribavirin. Virus Evolution 3, 2, vex035 (2017).
Q. Zhong, A. Carratalà, H. Shim, V. Bachmann, J.D. Jensen, T. Kohn. Resistance of echovirus 11 to CIO2 is associated with enhanced host receptor use, altered entry routes and high fitness. Environ. Sci. Technol. 51, 10746-10755 (2017).
population genetics; time-sampled data; approximate Bayesian computation; Wright-Fisher model; time-serial mutation rate analysis; time-serial effective population size analysis; time-serial selection analysis
see Example_diploid_model.R
see Example_haploid_model.R
Hyunjin Shim [[email protected]]