Hi @juan_dc. These files are output as part of running “augur traits”, which is effectively a wrapper around TreeTime’s “mugration” model. In a trait model, the rate of transition from states A→B, A→C, etc… is estimated. The mugration_model.txt output is pairwise matrix listing these rates. These pairwise rates should be largely comparable to pairwise rates estimated by BEAST using a standard phylogeographic model.
In addition, you get a JSON file that gives estimated locations of internal nodes in the tree and relative probability of these locations.