Dear Noor

As far as I understood from your question, you have already built a phylogenetic tree based on your sequences. If so, I think that the best way would be to reconstruct demographic history for each obtained clade. Please find attached a practical tutorial that would help you with BSP analysis. I attached also an interesting review paper by Ho and Shapiro (2011) on the issue.

I hope this would be helpful.

Dear Deli,

This method does not give me a plot that shows Pakistani HCV growth. How to get that? DO i have to make a tree that consists of Pakistani sequences only?

If you want to reconstruct demographic history for Pakistani samples, you have obviously to focus only on Pakistani sequences. But before making BSP analysis, why don't you investigate signatures of population demographic changes using neutrality tests such as Tajima’s D , Fu’s Fs , and Ramos-Onsins and Rozas R2. You can also examine site mismatch distributions which yield insight into past population demographics. BSP analysis would then provide a realistic population size function and enable retrieval of more details than just summary statistics.

thankyou . It helped alot