Or, as a minor variant of the code posted by moritz 
use strict;
use warnings;

my %pairs;
while (<DATA>) {
    my @names = split;
    # my @names = sort split;    # if order shouldn't matter
    while ( @names > 1 ) {
        my $first = shift(@names);
        map { ++$pairs{ join '_', $first, $_ } } @names;
    }
}
while ( my ( $k, $v ) = each %pairs ) {
    print "$k: $v\n";
}

__DATA__
tomD gly4 phil
aesG tomD gly4 phil
aesG phil
aesG tomD gly4

[download]

In reply to Re: counting pairwise incidences by jpl
in thread counting pairwise incidences by reubs85

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