[adegenet-forum] sPCA with sequence data

[Sofie Vandewoestijne]

Dear All,
I would like to combine PCA and geographic information (as in sPCA) 
using sequence data (I don't have genotype data available). Is this 
possible, for example by transforming polymorphic sites into SNP 
genotypes (but problem with linkage disequilibrium (?))? If so, how? 
If not, can anyone suggest an alternative technique?
Thank you!
Have a nice day,
Sofie

Sofie Vandewoestijne
Postdoctoral fellow
Biodiversity Research Centre
Catholic University Louvain
Place Croix du Sud 5
B-1348 Louvain-la-Neuve
Belgium

Tel: 32 (0)10 473454
Fax: 32 (0)10 473490

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