I have sequenced part of a gene for several individuals in several populations, and have scored SNP in them with BioEdit. I have then used PHASE in DNaSP to get the alleles.

From DNaSP I have saved the phased data to arlequin format, and in Arlequin i have then calculated measures such as Tajima D's and Fst on haplotype frequencies.

However, I need measures such as allelic richness and number of private alleles per population. I have found that the program FSTAT can calculate allelic richness. However, I can not figure out how to get my data to a format that FSTAT can read.

I have tried to use the program PGDspider2, however when I import FASTA data into here and try to convert it to FSTAT, I get the error "FSTAT needs diploid data!!!". But what format should the diploid FASTA data be in?

I can only see two obvious possibilites. Here er two examples:

1)

>Ind1

AMGTGC

>Ind2

AMGTRC

>Ind3

ACGTAC

... but this can only be unphased data.

2)

>Ind1-1

AAGTGC

>Ind1-2

ACGTGC

>Ind2-1

ACGTGC

>Ind2-2

AAGTAC

>Ind3-1

ACGTAC

>Ind3-2

ACGTAC

... which is phased data, and is what I get when I export as FASTA from DNaSP.

However, I cannot get PGDspider2 to recognize either of the two and get the same error each time.

In which format should the FASTA data be, in order to be able to convert it to FSTAT format?