Thanks for the response. I have a follow up question for you. The manuscript by DG Higgins (1992) states that principal coordinates analysis is superior to principal components analysis for sequence data. Do you have any thoughts on this or possibly a rationale for using principal components analysis in Jalview over the other option? I’ve been trying to play with both types of analysis on the same dataset and it does appear that I have better resolution of my data with the PCA implemented by Jalview.
Also, the same manuscript suggests that sequence ordinations are a great complement to phylogenetic analysis. In particular, Higgins states that sequence ordinations are important for gathering information about the deep branches of a phylogeny, while the phylogeny itself is better at describing the closely related neighboring sequences within a branch. Do you agree with this?