Running the programs

Programs in the PHASE package are run through the command line under both Unix-like systems and MS-windows systems. For Windows operating systems, you have to open a MS-DOS command window to use them. Click on ``Run...'' in the ``Start...'' menu and type cmd in the newly opened dialog box. You might have to type command instead of cmd depending on your MS-Windows version. Once the command window is opened, you have to move to the directory where you extracted the software. At the shell prompt, you can type, for example, cd c:$\backslash$Phase$\backslash$. You can then run any program of the PHASE package.

Run the programs by typing their name followed by the arguments they require. In most cases, PHASE's programs take one argument which is the name of a control file. You can type for instance:
mcmcphase control$\backslash$hiv-dna-mcmc-1.control or,
optimise control/primates-rna-optimise-7a.control
After installation, if the examples are all present, these commands should work.