Haplotype sequence data format

[Raul]

Greetings,

Am attempting to use Structure to analyze multi-locus data. I have
microsatellite data formatted with Genepop and that works well on its
own in Structure but am not sure how to add sequencing or haplotype
data to this existing file. Can you point me to an example file
perhaps or other? Thank you. Raul

[Jonathan Pritchard]

Sequencing or haplotype data are potentially problematic because they
usually violate the assumption of no LD between sites. However, if
you have data from enough independent regions this may still allow
accurate inference (eg see example from Conrad et al Nature Genetics
2006, Supp Info or Falush et al, Science 2003).

To enter sequence/haplotype data, simply treat each segregating site
as an independent locus and use usual Structure input format.

jonathan

[Raul]

thank you! appreciate your assistance, raul