This is probably a bit long-winded but does seem to work: 
my (@names,%hash,%matrix);

while (my $line = <DATA>)  {
    chomp($line);
    my ($name,$list) = split(m/\s+/,$line);
    push(@names,$name);
    $hash{$name} = [ split(',',$list) ];
}

for my $name (@names) {
    my $countries = $hash{$name};
    for my $name2 (@names) {
        my $diff = get_diff($countries,$hash{$name2});
        push( @{ $matrix{$name} }, $diff );
    }
}

sub get_diff {
    my ($x,$y) = @_;
    my (%union,%isect);
    for my $item (@$x,@$y) {
        $union{$item}++ && $isect{$item}++;
    }
    return scalar @$x - scalar keys %isect;
}

print "ID\t" . join("\t",@names) . "\n";
for my $name (@names) {
    print "$name\t" . join("\t", @{ $matrix{$name} } ) . "\n";
}

__DATA__
Name1  USA,Canada,Yemen 
Name2  Canada,Portugal,India
Name3  China,HongKong,Canada
Name4  London,Amsterdam,Ireland,USA
Name5  India,USA,Canada

[download]
Output: 
ID    Name1    Name2    Name3    Name4    Name5
Name1    0    2    2    2    1
Name2    2    0    2    3    1
Name3    2    2    0    3    2
Name4    3    4    4    0    3
Name5    1    1    2    2    0

[download]

In reply to Re: Doing pair-exclusivity analysis and building a matrix by tangent
in thread Doing pair-exclusivity analysis and building a matrix by angerusso

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