Testing For Selection In Quasispecies

Question

[Stevie Wonder]

Any suggestions for comparing groups of quasispecies clones looking for selection?

Many papers use raw dN/dS data but this seems at best a crude estimate given that the selection either for or against minor lineages may be underestimated.

Sliding window analysis also may be prone to this.

I have been using the codon based z test of selection in MEGA5 but feel that this again does not adequately consider the quasispecies nature of my data.

Any suggestions with regard to software or methodology greatly appreciated

Answer 1

[Zev.Kronenberg]

How about FST? You only need allele frequencies.