Phylodynamic network analysis using pairwise epidemic and coalescent models implemented in BEAST 2.
For a description of the pairwise coalescent model, see http://dx.doi.org/10.1101/082966
The examples folder contains XML files that can be run in BEAST 2, including simulated phylogenetic trees that were used to test the implementation of the model.
To replicate the analysis of the Swiss HIV-1 sub-epidemic, run BEAST using the input XML file 'SHC_MSM_pol_CH_subEpiTree_581_gammaNetReparam_noSeqs.xml'