SUMMARY OF THE COMMAND LINE USAGE

Clustal W is designed to be run interactively.  However, there are many
situations where it is convenient to run it from the command line, especially
if you wish to run it from another piece of software (e.g. SeqApp or GDE).
All parameters can be set from the command line by giving options after the
clustalw command. On UNIX options should be preceded by '-'.

If anything is put on the command line, the program will (attempt to) carry
out whatever is requested and will exit.  If you wish to use the command
line to set some parameters and then go into interactive mode, use the
command line switch: interactive .... e.g.

clustalw -quicktree -interactive    on UNIX

will set the default initial alignment mode to fast/approximate and will then
go to the main menu.


To see a list of all the command line parameters, type:

clustalw -options           on UNIX

and you will see a list with no explanation.
                                                                                             
To get (VERY BRIEF) help on command line usage, use the /HELP or /CHECK
(-help or -check on UNIX systems) options.