Looks like ab ac ad to me, in which case it simplifies to: 
use strict;
use warnings;

my %pairs;
while (<DATA>) {
    my ($first, @names) = split;
    for my $second (@names) {
        my $p = join '_', $first, $second;
        ++$pairs{$p};
    }
}
while (my ($k, $v) = each %pairs) {
    print "$k: $v\n";
}

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

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In reply to Re^2: counting pairwise incidences by ikegami
in thread counting pairwise incidences by reubs85

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