Analyses of the West Nile Virus data set and the simulated data sets presented in the manuscript can be executed using the version of PhyML available from from https://github.com/stephaneguindon/phyml.

Retrieve the code using the following commands (git needs to be installed on your computer):

          
            git clone https://github.com/stephaneguindon/phyml.git;
            cd ./phyml/;
            git checkout 009d3421b2d859868e7668d304d38cba4eda02ba
          
          

Compilation of PhyREX should be conducted using the following commands:

          
            sh ./autogen.sh;
            ./configure --enable-phyrex;
            make clean;
            make;
          
        

Running PhyREX to reproduce the analysis of the West Nile Virus data set first requires downloading the sequence alignment file, the coordinates and two XML configuration files (please run these commands from the src/ directory):

          
            wget http://stephaneguindon.github.io/WNV_lat_long.txt;
            wget http://stephaneguindon.github.io/WNV.phy;
            wget http://stephaneguindon.github.io/WNV_detection.xml;            
            wget http://stephaneguindon.github.io/WNV_survey.xml;            
          
        

Running the analysis under the detection scheme can then be done as follows (from the src/ directory):

          
            ./phyrex --xml=./WNV_detection.xml
          
        

Under the selection scheme :

          
            ./phyrex --xml=./WNV_selection.xml