Running and Verifying CAFE

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to switch to the directory where the test case is stored:

   cd /path/to/CAFE/CAFExp-5.0b2/examples

3. Run the following commands to run the case:

   ../bin/cafexp -t mammals_tree.txt -i mammal_gene_families.txt -o singlelambda

4. After the commands are executed, the following information is displayed:

   Completed 24 iterations
   Time: 0H 0M 7S
   Best match is: 0.0018174666100378
   Final -lnL: 164769.22040255
   47 values were attempted (0% rejected)
   
   Inferring processes for Base model
   Score (-lnL): 164769.22040255
   Computing pvalues...done!
   Starting reconstruction processes for Base model
   Done!