Dear Jalview community,
I have used the PCA option on a moderately large alignment (approx. 150 sequences, many of which are very similar). The 3D viewer shows three axes which I assume indicate the directions of the currently selected principal components. Clusters are clearly visible, but what I find irritating is that the axes are not mutually orthogonal. They do appear orthogonal when using the tutorial sequences, and this is still the case when I use my sequences unaligned, but not after proper alignment.
Is this an expected effect for an alignment of (at least cluster-wise) highly conserved sequences? And if yes, which coordinate system do the “transformed points” refer to? Would it be appropriate to simply plot those coordinates in an orthogonal frame?
Thanks a lot for any pointer!
Best regards,
Oliver