This

 tempProteinFamFileCreator();
...
sub tempProteinFamFileCreator 
{
my $infile = $ARGV[0]."_ProFam";
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is more generically written as

...
tempProteinFamFileCreator( @ARGV );
...
sub tempProteinFamFileCreator {
    my  $infile   = $_[0] .'_ProFam';
# or
#   my  $infile   = shift .'_ProFam';


...
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Now sub tempProteinFamFileCreator doesn't depend on @ARGV :) after all, you wouldn't write

 @ARGV = ( 1 , 2 , 3 );
print @ARGV;
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instead of

print 1,2,3;
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