Hello guys,

I have a flu dataset for which we would like to look at evolutionarily conserved sites, similar to the analysis done in:

Ngandu, N. K., Scheffler, K., Moore, P., Woodman, Z., Martin, D., & Seoighe, C. (2008). Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences. Virology Journal, 5, 160.

with HIV data. Is there any way to perform such analysis with the current HyPhy version? if yes, what would be the batch file? If not, is there any way to get the batch file used?

Thanks in advance

Ed

Hi Ed,

There is a sliding window analysis in HyPhy -- Standard Analyses:Miscellaneous:SlidingWindowAnalysis.bf
I would give that a try with a locally parameterized codon model.

Sergei

Thanks Sergei!

Ed