Population structure

In this notebook, we run a principal components analysis and build a neighbour joining tree on the amplicon sequencing variant data. For the PCA, we will plot PC1 v PC2 and PC3 v PC4, and the variance explained by the model.

Variance explained

As a general rule of thumb, when the variance explained for each PC begins to flatten out, that is when the PCs are no longer informative.

PCA

NJT

excluding extreme outliers from NJT []