Compiling and Installing PAML

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to decompress the PMAL installation package:

   tar xf paml4.9j.tgz

3. Run the following command to switch to the directory generated after decompression:

   cd paml4.9j

4. Run the following commands to delete the Windows executable file (.exe file) from the paml4.9j/bin/ folder:

   cd /path/to/PAML/paml4.9j/bin

   rm *.exe

5. Run the following commands to perform compilation:

   cd /path/to/PAML/paml4.9j/src

   make -f Makefile

   ls -lF

   rm *.o

6. Run the following commands to copy the executable file in the src directory to the bin directory:

   cp /path/to/PAML/paml4.9j/src/baseml basemlg codeml pamp evolver yn00 chi2 /path/to/PAML/paml4.9j/bin

   cd ..

   ls -lF bin

   If the following three files exist in the bin directory, the compilation is successful:

   bin/baseml
   bin/codeml
   bin/evolver