timblokker / phycova Goto Github PK

Hello, I am trying to use PhyCovA for my dataset. I have an ML tree with annotations for ancestral states. I cannot use this tree since it is not in the BEAST format for ancestral states, and it seems very complicated to reformat from a Newick annotated tree to one that would be accepted as a BEAST format.

Alternatively, since this is just for a test of association, I can use the character reconstruction that is part of the application. This, however, required ordered tip states. I do not understand the order that these should be in. I have input my newick ML tree. I also have the matrix complete. I just need to input somewhere the accession numbers and their associated locations. I'm assuming this would be input in 'Sampling locations'. But it seems this only accepts a file with one column with tip locations in order. My question is, what is this order supposed to be based off.

Thank you for your help.

All the best-
Andrew