[adegenet-forum] Fst for mitochondrial DNA

[Stefan Prost]

Hello,

 I would like to calculate Fst's for 25 populations (all in all about 1200
complete mitochondrial genomes). I used the pairwise.fst function from
adegenet, but got NA's in the results and warnings

In df2genind(tab, pop = pop, ploidy = x[[1]]@ploidy, type = x[[1]]@type) :
 entirely non-type marker(s) deleted


All sequences should be ploidy 1 and type codom.

Any ideas why it calculates the FST for some, but by far not all
populations? Is that a data input problem or something else?

Thanks for the help!

Best,
Stefan