BEsTRF.exe is the executable file for T-RFLP space exploration
which finds a set of primers with highest sampling capacity, 
generating highest number of peaks after restriction enzyme digestion
resulting in highest T-RFLP resolution based on input sequences.



;*******************************************************************
;
; V. Running the application
;
;*******************************************************************



;
; How to run the program in MS(R) Windows(TM) and Linux(R)?
;
; A.  Download the appropriate ZIP archive.
;
; B.  Unpack the ZIP archive into the folder/directory
;     of your choice.
;
; C.  Have your FASTA sequences at hand (on your local disk).
;
; D.  Prepare parameters file (like this one) according to your
;     specifications and desires.
;
;
;
;     ***** Windows specific *****
;
; E.  Double click on the EXE file to start the program.
;
; F.  When the program asks you for the name of the file with
;     parameters (the one that you have prepared in step "D"),
;     properly satisfy its curiosity.
;
; G.  Grab a cup of coffee, some lunch, or go to vacation,
;     depending on an imposed workload.
;     
; H.  Use the results of the analysis in whatever way you like.
;     Examine directory log_of_analysis that contains
;     progress report and other files that reveal level of success.
;
;
;     
;     ***** Linux specific *****
;
;     In Linux you usualy do not have the possibility of the first
;     approach that we described for Windows because graphics
;     user interfaces do not let you double click on an executable
;     to run it. Instead, you must resort to the analogy of the
;     second aproach.
;
; E.  Open "Terminal Window" or "Linux Console" into the directory
;     with program executable. Do this by selecting the appropriate
;     choice in a menu of your GUI "Linux explorer"
;     (like Dolphin if you are using KDE(R) desktop environment).
;     Note that in Linux it is usually possible by default to open
;     the terminal window directly into the directory of
;     your choice.
;
; F.  Start the program by entering the following command:
;
;     ./BEsTRF_version   your_parameter_file.txt
;
;     ...note the sequence of characters "./" at the beginning
;        of the line, which you must not forget;
;
;     Alternatively, you can copy program executable into some
;     directory on the PATH (usually, a suitable choice 
;     is "/usr/local/bin"), so that you can execute it from any
;     directory and without the annoying sequence "./".
;
; G.  Grab a cup of coffee, some lunch, or go to vacation,
;     depending on an imposed workload.
;     
; H.  Use the results of the analysis in whatever way you like.
;     Examine directory log_of_analysis that contains
;     progress report and other files that reveal level of success.
;