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value is C<undef>. Here you should take care how you test. For example:

 if ( ! $node->get_parent ) {
 	$root = $node;
 }

This works as expected - object references are always "true", so if
C<get_parent> returns "false", C<$node> has no parent - hence it must 
be the root. However:

 if ( ! $node->get_branch_length ) {

 	# is there really no branch length?
 	if ( defined $node->get_branch_length ) {

 		# perhaps there is, but of length 0.
 	}
 }

...warrants caution. Zero is evaluated as false-but-defined.

=back

=head2 Exceptions

The Bio::Phylo modules throw exceptions that subclass L<Exception::Class>.
Exceptions are thrown when something I<exceptional> has happened. Not when the
value requested through an accessor method is undefined. If a node has no
parent, C<undef> is returned. Usually, you will encounter exceptions in
response to invalid input.

=over

=item Trying/Catching exceptions

If some method call returns an exception, wrap the call inside an C<eval>
block. The error now becomes non-fatal:

 # try something:
 eval { $node->set_branch_length('a bad value'); };

 # handle exception, if any
 if ($@) {
    # do something, e.g.:
    print $@->trace->as_string; # <- $@ is an object!
 }

=item Stack traces

If an exception of a particular type is caught, you can print a stack trace
and find out what might have gone wrong starting from your script drilling
into the module code.

 # exception caught.
 if ( UNIVERSAL::isa( $@, 'Bio::Phylo::Util::Exceptions::BadNumber' ) ) {

    # prints stack trace in addition to error
    warn $@->error, "\n, $@->trace->as_string, "\n";

    # further metadata from exception object
    warn join ' ',  $@->euid, $@->egid, $@->uid, $@->gid, $@->pid, $@->time;
    exit;
 }

As a new feature (from v.0.17 onwards) exceptions have become more descriptive,
with a generic explanation of what the thrown exception class typically means
added to the error message, and stack traces are printed out by default.

=item Exception types

Several exception classes are defined. The type of the thrown exception should
give you a hint as to what might be wrong. The types are specified in the
L<Bio::Phylo::Util::Exceptions> perldoc.

=back

=head1 TO DO

Below is a list of things that hopefully will be implemented in future 
versions of Bio::Phylo.

=over

=item More DNA sequence methods

Such as $seq->complement;. This would imply larger constant translation 
tables, including various tables for mtDNA and so on. Will probably be 
implemented, must likely using BioPerl tools.

=item Databases

Implement/improve access to TreeBASE, TolWeb and other databases. This could
probably be done best using PhyloWS.

=item Tests

Test coverage is reasonable, but some of the newer features need to be exercised
more.

=item Interoperability with BioPerl

The eventual aim of the Bio::Phylo project is to glue together the phylogenetics 
aspects of BioPerl (L<http://www.bioperl.org>), L<Bio::NEXUS>.

=back

=head1 FORUM

CPAN hosts a discussion forum for Bio::Phylo. If you have trouble
using this module the discussion forum is a good place to start
posting questions (NOT bug reports, see below):
L<http://www.cpanforum.com/dist/Bio-Phylo>

=head1 BUGS

Please report any bugs or feature requests to C<< bug-bio-phylo@rt.cpan.org >>,
or through the web interface at
L<http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo>. I will be notified,
and then you'll automatically be notified of progress on your bug as I make
changes.