I can't phase my data. What can I do with it?

Question

[javiercalvelo7]

Hello. Here is my problem:

I'm trying to analyse the population structure of a catfish but PHASE 2.1 fails to recover good candidate pairs for one nuclear gene for most of my dataset of 51 individuals. The reason, I think, are two SNP (T/C and G/C) for which the four possible combinations are actually present. I have at least one homozygote for each.

There is any program that can deal with this kind of data? What analysis do you recommend?

Thanks.

Answer 1

[Brice Sarver]

Is your goal just to answer questions about population structure? Try ADMIXTURE or STRUCTURE.

You would also be justified in excluding multiallelic sites since they violate the infinite sites model and, therefore, might violate the assumptions of the models underlying the programs you are trying to run.