tomD gly4 phil
aesG tomD gly4 phil  
aesG phil 
aesG tomD gly4 
etc...

##</code><code>##

aesG_tomD = 1
aesG_gly4 = 1
aesG_phil = 1
tomD_gly4 = 2
tomD_phil = 2
gly4_phil = 2

##</code><code>##

my $tomD_phil;
etc...

foreach (@line_of_input_file) {

  if (($_ =~ /tomD/) and ($_ =~ /phil/)) { $tomD_phil++ }
  etc...  
}