Hi,
I read a article about Campylobacter fetus that is a multi-host bacterial pathogen.And C. fetus cat jump into different host-species populations.To infer the host-to-host transmission patterns of C. fetus,this article reconstructed the ancestral states for the internal nodes of the phylogeny and quantified each specific type of host transmission.
I have similar data for another multi-host bacterial pathogen.I also want to quantified each specific type of host transmission and get a graph like Figure 1c of the above article.According to the method of this article,I used the BEAST v1.7.5 package to jointly estimate the substitution rate, a dated phylogeny and the reconstruction of host ancestral states using a continuous-time Markov chain(CTMC) discrete model.I get the Log File and Tree File by running BEAST,but I don't know how to get the transmission rate and the Bayes factor of each host transmission.
Thanks a lot, hope to get your suggestions!
The article link:https://www.nature.com/articles/s41467-017-01449-9
