You can specify options or commands through the command line. You can also run the program in an interactive mode where you can type commands. The command line format is as follows:
unialign.exe "option1 value1" "option2 value2" "command1" "command2 argument2 argument3" ...
Equivalently, you can type the same commands in interactive mode:
unialign.exe "cmdmode 1" > option1 value1 > option2 value2 > command1 > command2 argument2 argument3