POPGENOME: fasta input

Question

[gentiaco]

Hi everyone,

I have generated a Multiple Sequence alignment of a gene from different ecotypes and I would like to perform some population genetics tests to study and detect the signature of evolution. In order to do that, I am using POPGENOME on R, following the tutorial https://github.com/tonig-evo/workshop-popgenome and the manual. It seems that the readData("...") function uploads the fasta file without any problems. However, when I run the get.sum.data() function, only the number of sites are counted, whereas the number of gaps, biallelic sites, valid sites and ambiguous sites (etc.) are reported as 0. thus, it is impossible to perform further tests. Do you know why this occurs? is it a problem with the format of the alignment?

regards

[brianagross]

Did you ever figure this out? I am having exactly the same problem!