genetic differences among populations defined by population analysis

[kopelol]

genetic differences among populations defined by population analysis

[kopelol]

In addition, I tried to use "--no_pairwise", but the results was same before using this option.

[AdmiralenOla]

Hi @kopelol .

In this case you should just use your 6 already specified populations from your previous analysis. Note that you will have to create 6 individual phenotype variables and then have a binary membership. Example:

,Pop1,Pop2,Pop3,Pop4,Pop5,Pop6
Strain1,1,0,0,0,0,0
Strain2,0,0,0,1,0,0
etc.

Using "--no_pairwise" should make your analysis run quicker since you are noe performing any pairwise comparisons, that is, you are not correcting for population structure at all. In these analyses it doesn't actually matter if you use a pre-defined newick tree or let this be handled internally by Scoary.