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=item calc_split_frequency()

Calculates frequency of provided split

 Type    : Calculation
 Title   : calc_split_frequency
 Usage   : my $freq = $trees->calc_split_frequency([$node1,$node2]);
 Function: Calculates split frequency
 Returns : Scalar, a number
 Args    : An array of taxon objects, or a taxa object
 Comment :

=cut

    sub calc_split_frequency {
        my ( $self, $arg ) = @_;
        my @trees  = @{ $self->get_entities };
        my $ntrees = scalar @trees;
        if ($ntrees) {
            my $count = 0;
            for my $tree (@trees) {
                $count++ if $tree->is_clade($arg);
            }
            return $count / $ntrees;
        }
        return 0;
    }

=back

=head1 METHODS

=over

=item insert()

Inserts trees in forest.

 Type    : Method
 Title   : insert
 Usage   : $trees->insert( $tree1, $tree2, ... );
 Function: Inserts trees in forest.
 Returns : A Bio::Phylo::Forest object.
 Args    : Trees
 Comment : The last seen tree that is set as default
           becomes the default for the entire forest

=cut

    sub insert {
        my $self = shift;
        if ( $self->can_contain(@_) ) {
            my $seen_default = 0;
            for my $tree ( reverse @_ ) {
                if ( $tree->is_default ) {
                    if ( not $seen_default ) {
                        $seen_default++;
                    }
                    else {
                        $tree->set_not_default;
                    }
                }
            }
            if ($seen_default) {
                if ( my $tree = $self->get_default_tree ) {
                    $tree->set_not_default;
                }
            }
            $self->SUPER::insert(@_);
        }
        else {
            throw 'ObjectMismatch' => "Failed insertion: @_ [in $self]";
        }
    }

=item get_default_tree()

Gets the default tree in the forest.

 Type    : Method
 Title   : get_default_tree
 Usage   : my $tree = $trees->get_default_tree;
 Function: Gets the default tree in the forest.
 Returns : A Bio::Phylo::Forest::Tree object.
 Args    : None
 Comment : If no default tree has been set, 
           returns first tree. 

=cut

    sub get_default_tree {
        my $self  = shift;
        my $first = $self->first;
        for my $tree ( @{ $self->get_entities } ) {
            return $tree if $tree->is_default;
        }
        return $first;
    }

=item check_taxa()

Validates taxon links of nodes in invocant's trees.

 Type    : Method
 Title   : check_taxa
 Usage   : $trees->check_taxa;
 Function: Validates the taxon links of the
           nodes of the trees in $trees
 Returns : A validated Bio::Phylo::Forest object.
 Args    : None

=cut

    sub check_taxa {
        my $self = shift;

        # is linked
        if ( my $taxa = $self->get_taxa ) {
            my %tips;
			
			# build a hash of all the unlinked tips by their names
            TIP: for my $tip ( map { @{ $_->get_terminals } } @{ $self->get_entities } ) {
				next TIP if $tip->get_taxon && $taxa->contains($tip->get_taxon);
                my $name = $tip->get_internal_name;
                if ( not $tips{$name} ) {
                    $tips{$name} = [];