Hi all,
I am trying to use SPAGEDI v 1.5 to compare RST and FST statistics by pRst. However, the manual is not helpful on how I can compute these calculations. Would anyone know what steps to follow?
Thanks and best regards
Michael J. Jowers
Hi Michael,
First you have to choose categorical groups, then you choose the genetic structure index you want, reamember that permutation test is only available for statistics based on allele size and based on distance between alelles, once you decide the distances, you choose the permutation test option and the type of permutation, finally you only have to define if you need the distance matrix, diversity per populations and other format options.
At the end in you output you should observe the (lets say) GST, RST and NST values and below the observed/mean permutated values of the "location individulas or genes permutation", finally, if you choose the allele permutation once again below you will only observe the NST and GST observed/mean permuted values with the P for one side or two sided test.
The sequence of options should be like:
input
ouput
2 (categorical)
e.g. 368 (GST, RST and NST)
return if you have the distance in the input file
3 (permutation test)
12 (permuting gene copies/individuals/locations and allels)
return
no. permutations
14 for diversity per populations (if you need it) and matrices
4 matrices in columns and matrix
Saludos!
Hernando,
I am so sorry, I never got to thank you regarding my question on Spagedi!! I just realized! Many thanks and very much apperciated!
Muchas gracias!
Michael
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