This repository contains 3 branches, the master branch can be used to build the application from source. The dockerhub branch leads to a docker image that can be pulled from timblokker/phycova_treetime from dockerhub. The heroku branch is also leading to a docker image on dockerhub but does not include the treetime software and is not suited to be run locally but is instead collected from dockerhub by heroku automatically. The application cen be accessed via the application referenced under environments.
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.