
                          X! tandem protein sequence modeler

  Installation
  -----------
  This distribution contains three directories:
  
  1. src   - contains the source files for tandem. To compile this program, first determine
  		if you are using the 32-bit or 64-bit version of Linux. 
  		- change directory into the /src directory in a terminal window.

   		- for for most types of Linux, using GCC version 4, type
   		">make" or
  		">make -f Makefile_GCCv4_P3"

  		- for most types of Linux that still use GCC version 3, type
  		">make -f Makefile_GCCv3" or
  		">make -f Makefile_GCCv3_P3"

 		- for 32-bit Ubuntu, type
  		">make -f Makefile_Ubuntu_32" or
  		">make -f Makefile_Ubuntu_P3_32"

  		- for 64-bit Ubuntu, type
   		">make -f Makefile_Ubuntu" or
  		">make -f Makefile_Ubuntu_P3".

  		- the new compiled programs with be in the /bin directory.
 
  2. bin   - contains the binary for tandem, as well as example
             files and mass spectra. You can run tandem
             from the command line in this directory, by using the 
             command line:
            
             >tandem input.xml
            
             The output from the program will appear in the output file
             specified. Check the path names in taxonomy.xml and input.xml
             if there is trouble doing this check. Read the default_input.xml
             file for more information on how the input parameter file format
             works.
            
  3. fasta - contains an example FASTA protein sequence list file. This
             type of file is often refered to as a "database" file or
             simply a "database". However, it is not a database of any
             type: it is simply a file with a simple (but poorly specified)
             format.
  
 
