Virus evolution simulation

A virus sequence and its genomic structure is the result of a complex set of factors like mutations, insertion-deletions and selection at different levels such as RNA secondary structure and protein structure. It is feasible to make a simulator that incorporates all these factors and this would allow investigation of how these factors contribute to the structure of real viruses and address questions such as why is the amount of overlap in reading frames as it is? How much selections is there on conserved RNA structure relative to protein structure? How realiably can selection be detected by sequence comparison?