Hi,
I am doing an analysis to infer the convergent evolution of bacteria in a longitudinal study.
Several clones of the same bacterium are studied to determine whether they have within-host convergent evolution. For each clone, samples were collected from different time points. It is kind of similar idea to this research #62 .
If I want to analyze whether there is convergent evolution that occurs among several clones, what is the best method I should use?

1. Should I call SNP and use the original SNPGenie or should I use the within-group with the msa? If I use msa instead of vcf, would it be overkill like the situation described here? analysing within-host diversity #44
2. Will VCFGenie be helpful in this case?

Thank you so much for your help!