chak:~$ phylip sub_program_1
sub_program_1: the file "out-file" that you wanted to use as output 
file already exists. Do you want to Replace it, Append to it, write 
to a new File, or Quit? (please type R, A, F, or Q)
.....
(phylip subprogram_2
......
please type R, A, F, or Q) n times