Which is the most appropriate graphical method to represent distances between breeds concerning one locus?

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Binod Regmi

If you estimate Fst, Visualization with PCoA makes more sense than just using a dendrogram.

Hossem SAHRAOUI

Thank you dear Binod! You're answer is interesting!

Ali Raza

For me both are fine. As you want to show distance based on polymorphism, so you must show results in both graphs. It would be very nice presentation.

But I will prefer PCA over dendrogram, if you want to choose one of them.