Cool - We get a chance to use the "seldom used" ForceContent=>1 and ContentKey=>'keyname' options of XMLin. :-)

use XML::Simple;

sub parse_newick {
    local $_ = shift;
    s<[(]>[<LEFT>]g; s<[,]>[</LEFT><RIGHT>]g; s<[)]>[</RIGHT>]g;
    XMLin "<opt>$_</opt>", ForceContent => 1, ContentKey => 'VALUE';
}

use Data::Dumper;
print Dumper parse_newick( '(A,(B,C))' );
[download]