Hello!

my student and I are working on implementing PCA analysis on my viral sequence dataset for her applied math course. It will be fun to see if/how her results compare to my compartmentalization analysis via HyPhy!

We need to calculate the relative diversity of each isolate's sequence (versus the entire population) so she can use that in her PCA matrix. I know HyPhy will do that with many methods for various analyses, but I don't know if it will actually give me that data in a format she and I can use.

she has seen that many people use dN/dS ratios for this measure, but we don't think that's the best idea. We're thinking along the lines of a simple pairwise calculation.

thoughts are welcome and appreciated! thank you

Hi rbjmax,

Your best bet is probably a matrix of pairwise distances which can be generated in a variety of formats, all machine readable, using the file TemplateBatchFiles/DistanceMatrix.bf

You can either access it directly or through Standard Analyses:Phylogeny Reconstruction:DistanceMatrix.bf

Sergei

thank you, again, Sergei!
Rachel