Bio::Phylo::Forest::TreeRole - Extra behaviours for a phylogenetic tree
# some way to get a tree
use Bio::Phylo::IO;
my $string = '((A,B),C);';
my $forest = Bio::Phylo::IO->parse(
-format => 'newick',
-string => $string
);
my $tree = $forest->first;
# do something:
print $tree->calc_imbalance;
# prints "1"
The object models a phylogenetic tree, a container of Bio::Phylo::Forest::Node objects. The tree object inherits from Bio::Phylo::Listable, so look there for more methods.
Tree constructor.
Type : Constructor Title : new Usage : my $tree = Bio::Phylo::Forest::Tree->new; Function: Instantiates a Bio::Phylo::Forest::Tree object. Returns : A Bio::Phylo::Forest::Tree object. Args : No required arguments.
Tree constructor from Bio::Tree::TreeI argument.
Type : Constructor
Title : new_from_bioperl
Usage : my $tree =
Bio::Phylo::Forest::Tree->new_from_bioperl(
$bptree
);
Function: Instantiates a
Bio::Phylo::Forest::Tree object.
Returns : A Bio::Phylo::Forest::Tree object.
Args : A tree that implements Bio::Tree::TreeI
Gets node that divides tree into two distance-balanced partitions.
Type : Query Title : get_midpoint Usage : my $midpoint = $tree->get_midpoint; Function: Gets node nearest to the middle of the longest path Returns : A Bio::Phylo::Forest::Node object. Args : NONE Comments: This algorithm was ported from ETE
Get terminal nodes.
Type : Query
Title : get_terminals
Usage : my @terminals = @{ $tree->get_terminals };
Function: Retrieves all terminal nodes in
the Bio::Phylo::Forest::Tree object.
Returns : An array reference of
Bio::Phylo::Forest::Node objects.
Args : NONE
Comments: If the tree is valid, this method
retrieves the same set of nodes as
$node->get_terminals($root). However,
because there is no recursion it may
be faster. Also, the node method by
the same name does not see orphans.
Get internal nodes.
Type : Query
Title : get_internals
Usage : my @internals = @{ $tree->get_internals };
Function: Retrieves all internal nodes
in the Bio::Phylo::Forest::Tree object.
Returns : An array reference of
Bio::Phylo::Forest::Node objects.
Args : NONE
Comments: If the tree is valid, this method
retrieves the same set of nodes as
$node->get_internals($root). However,
because there is no recursion it may
be faster. Also, the node method by
the same name does not see orphans.
Get all cherries, i.e. nodes that have two terminal children
Type : Query
Title : get_cherries
Usage : my @cherries = @{ $tree->get_cherries };
Function: Returns an array ref of cherries
Returns : ARRAY
Args : NONE
Gets a forest of all rooted versions of the invocant tree.
Type : Query
Title : get_all_rootings
Usage : my $forest = $tree->get_all_rootings;
Function: Returns an array ref of cherries
Returns : Bio::Phylo::Forest object
Args : NONE
Comments: This method assumes the invocant tree has a basal trichotomy.
"Rooted" trees with a basal bifurcation will give strange
results.
Get root node.
Type : Query Title : get_root Usage : my $root = $tree->get_root; Function: Returns the root node. Returns : Bio::Phylo::Forest::Node Args : NONE
Gets number of tips
Type : Query Title : get_ntax Usage : my $ntax = $tree->get_ntax; Function: Calculates the number of terminal nodes Returns : Int Args : NONE
Retrieves the node furthest from the root.
Type : Query
Title : get_tallest_tip
Usage : my $tip = $tree->get_tallest_tip;
Function: Retrieves the node furthest from the
root in the current Bio::Phylo::Forest::Tree
object.
Returns : Bio::Phylo::Forest::Node
Args : NONE
Comments: If the tree has branch lengths, the tallest tip is
based on root-to-tip path length, else it is based
on number of nodes to root
Gets node objects for the supplied taxon objects
Type : Query
Title : get_nodes_for_taxa
Usage : my @nodes = @{ $tree->get_nodes_for_taxa(\@taxa) };
Function: Gets node objects for the supplied taxon objects
Returns : array ref of Bio::Phylo::Forest::Node objects
Args : A reference to an array of Bio::Phylo::Taxa::Taxon objects
or a Bio::Phylo::Taxa object
Get most recent common ancestor of argument nodes.
Type : Query
Title : get_mrca
Usage : my $mrca = $tree->get_mrca(\@nodes);
Function: Retrieves the most recent
common ancestor of \@nodes
Returns : Bio::Phylo::Forest::Node
Args : A reference to an array of
Bio::Phylo::Forest::Node objects
in $tree.
Test if tree is bifurcating.
Type : Test
Title : is_binary
Usage : if ( $tree->is_binary ) {
# do something
}
Function: Tests whether the invocant
object is bifurcating.
Returns : BOOLEAN
Args : NONE
Test if tree is ultrametric.
Type : Test
Title : is_ultrametric
Usage : if ( $tree->is_ultrametric(0.01) ) {
# do something
}
Function: Tests whether the invocant is
ultrametric.
Returns : BOOLEAN
Args : Optional margin between pairwise
comparisons (default = 0).
Comments: The test is done by performing
all pairwise comparisons for
root-to-tip path lengths. Since many
programs introduce rounding errors
in branch lengths the optional argument is
available to test TRUE for nearly
ultrametric trees. For example, a value
of 0.01 indicates that no pairwise
comparison may differ by more than 1%.
Note: behaviour is undefined for
negative branch lengths.
Tests if first argument (node array ref) is monophyletic with respect to second argument.
Type : Test
Title : is_monophyletic
Usage : if ( $tree->is_monophyletic(\@tips, $node) ) {
# do something
}
Function: Tests whether the set of \@tips is
monophyletic w.r.t. $outgroup.
Returns : BOOLEAN
Args : A reference to a list of nodes, and a node.
Comments: This method is essentially the
same as
&Bio::Phylo::Forest::Node::is_outgroup_of.
Type : Test
Title : is_paraphyletic
Usage : if ( $tree->is_paraphyletic(\@nodes,$node) ){ }
Function: Tests whether or not a given set of nodes are paraphyletic
(representing the full clade) given an outgroup
Returns : [-1,0,1] , -1 if the group is not monophyletic
0 if the group is not paraphyletic
1 if the group is paraphyletic
Args : Array ref of node objects which are in the tree,
Outgroup to compare the nodes to
Tests if argument (node array ref) forms a clade.
Type : Test
Title : is_clade
Usage : if ( $tree->is_clade(\@tips) ) {
# do something
}
Function: Tests whether the set of
\@tips forms a clade
Returns : BOOLEAN
Args : A reference to an array of Bio::Phylo::Forest::Node objects, or a
reference to an array of Bio::Phylo::Taxa::Taxon objects, or a
Bio::Phylo::Taxa object
Comments:
Tests if tree is a cladogram (i.e. no branch lengths)
Type : Test
Title : is_cladogram
Usage : if ( $tree->is_cladogram() ) {
# do something
}
Function: Tests whether the tree is a
cladogram (i.e. no branch lengths)
Returns : BOOLEAN
Args : NONE
Comments:
Calculates the Euclidean branch length distance between two trees.
Type : Calculation
Title : calc_branch_length_distance
Usage : my $distance =
$tree1->calc_branch_length_distance($tree2);
Function: Calculates the Euclidean branch length distance between two trees
Returns : SCALAR, number
Args : NONE
Calculates the squared Euclidean branch length distance between two trees.
Type : Calculation
Title : calc_branch_length_score
Usage : my $score =
$tree1->calc_branch_length_score($tree2);
Function: Calculates the squared Euclidean branch
length distance between two trees
Returns : SCALAR, number
Args : NONE
Calculates the sum of all branch lengths.
Type : Calculation
Title : calc_tree_length
Usage : my $tree_length =
$tree->calc_tree_length;
Function: Calculates the sum of all branch
lengths (i.e. the tree length).
Returns : FLOAT
Args : NONE
Calculates the height of the tree.
Type : Calculation
Title : calc_tree_height
Usage : my $tree_height =
$tree->calc_tree_height;
Function: Calculates the height
of the tree.
Returns : FLOAT
Args : NONE
Comments: For ultrametric trees this
method returns the height, but
this is done by averaging over
all root-to-tip path lengths, so
for additive trees the result
should consequently be interpreted
differently.
Calculates the number of nodes.
Type : Calculation
Title : calc_number_of_nodes
Usage : my $number_of_nodes =
$tree->calc_number_of_nodes;
Function: Calculates the number of
nodes (internals AND terminals).
Returns : INT
Args : NONE
Calculates the number of terminal nodes.
Type : Calculation
Title : calc_number_of_terminals
Usage : my $number_of_terminals =
$tree->calc_number_of_terminals;
Function: Calculates the number
of terminal nodes.
Returns : INT
Args : NONE
Calculates the number of internal nodes.
Type : Calculation
Title : calc_number_of_internals
Usage : my $number_of_internals =
$tree->calc_number_of_internals;
Function: Calculates the number
of internal nodes.
Returns : INT
Args : NONE
Calculates the number of cherries, i.e. the number of nodes that subtend exactly two tips. See for applications of this metric: http://dx.doi.org/10.1016/S0025-5564(99)00060-7
Type : Calculation
Title : calc_number_of_cherries
Usage : my $number_of_cherries =
$tree->calc_number_of_cherries;
Function: Calculates the number of cherries
Returns : INT
Args : NONE
Calculates the sum of all root-to-tip path lengths.
Type : Calculation
Title : calc_total_paths
Usage : my $total_paths =
$tree->calc_total_paths;
Function: Calculates the sum of all
root-to-tip path lengths.
Returns : FLOAT
Args : NONE
Calculates the amount of shared (redundant) history on the total.
Type : Calculation
Title : calc_redundancy
Usage : my $redundancy =
$tree->calc_redundancy;
Function: Calculates the amount of shared
(redundant) history on the total.
Returns : FLOAT
Args : NONE
Comments: Redundancy is calculated as
1 / ( treelength - height / ( ntax * height - height ) )
Calculates Colless' coefficient of tree imbalance.
Type : Calculation
Title : calc_imbalance
Usage : my $imbalance = $tree->calc_imbalance;
Function: Calculates Colless' coefficient
of tree imbalance.
Returns : FLOAT
Args : NONE
Comments: As described in Colless, D.H., 1982.
The theory and practice of phylogenetic
systematics. Systematic Zoology 31(1): 100-104
Calculates I2 imbalance.
Type : Calculation Title : calc_i2 Usage : my $ci2 = $tree->calc_i2; Function: Calculates I2 imbalance. Returns : FLOAT Args : NONE Comments:
Calculates the Pybus gamma statistic.
Type : Calculation
Title : calc_gamma
Usage : my $gamma = $tree->calc_gamma();
Function: Calculates the Pybus gamma statistic
Returns : FLOAT
Args : NONE
Comments: As described in Pybus, O.G. and
Harvey, P.H., 2000. Testing
macro-evolutionary models using
incomplete molecular phylogenies.
Proc. R. Soc. Lond. B 267, 2267-2272
Calculates stemminess measure of Fiala and Sokal (1985).
Type : Calculation
Title : calc_fiala_stemminess
Usage : my $fiala_stemminess =
$tree->calc_fiala_stemminess;
Function: Calculates stemminess measure
Fiala and Sokal (1985).
Returns : FLOAT
Args : NONE
Comments: As described in Fiala, K.L. and
R.R. Sokal, 1985. Factors
determining the accuracy of
cladogram estimation: evaluation
using computer simulation.
Evolution, 39: 609-622
Calculates stemminess measure from Rohlf et al. (1990).
Type : Calculation
Title : calc_rohlf_stemminess
Usage : my $rohlf_stemminess =
$tree->calc_rohlf_stemminess;
Function: Calculates stemminess measure
from Rohlf et al. (1990).
Returns : FLOAT
Args : NONE
Comments: As described in Rohlf, F.J.,
W.S. Chang, R.R. Sokal, J. Kim,
1990. Accuracy of estimated
phylogenies: effects of tree
topology and evolutionary model.
Evolution, 44(6): 1671-1684
Calculates tree resolution.
Type : Calculation
Title : calc_resolution
Usage : my $resolution =
$tree->calc_resolution;
Function: Calculates the number
of internal nodes over the
total number of internal nodes
on a fully bifurcating
tree of the same size.
Returns : FLOAT
Args : NONE
Calculates cumulative branching times.
Type : Calculation
Title : calc_branching_times
Usage : my $branching_times =
$tree->calc_branching_times;
Function: Returns a two-dimensional array.
The first dimension consists of
the "records", so that in the
second dimension $AoA[$first][0]
contains the internal node references,
and $AoA[$first][1] the branching
time of the internal node. The
records are orderered from root to
tips by time from the origin.
Returns : SCALAR[][] or FALSE
Args : NONE
Calculates intervals between splits.
Type : Calculation
Title : calc_waiting_times
Usage : my $waitings =
$tree->calc_waiting_times;
Function: Returns a two-dimensional array.
The first dimension consists of
the "records", so that in the
second dimension $AoA[$first][0]
contains the internal node references,
and $AoA[$first][1] the waiting
time of the internal node. The
records are orderered from root to
tips by time from the origin.
Returns : SCALAR[][] or FALSE
Args : NONE
Calculates node ages.
Type : Calculation
Title : calc_node_ages
Usage : $tree->calc_node_ages;
Function: Calculates the age of all the nodes in the tree (i.e. the distance
from the tips) and assigns these to the 'age' slot, such that,
after calling this method, the age of any one node can be retrieved
by calling $node->get_generic('age');
Returns : The invocant
Args : NONE
Comments: This method computes, in a sense, the opposite of
calc_branching_times: here, we compute the distance from the tips
(i.e. how long ago the split occurred), whereas calc_branching_times
calculates the distance from the root.
Calculates lineage-through-time data points.
Type : Calculation
Title : calc_ltt
Usage : my $ltt = $tree->calc_ltt;
Function: Returns a two-dimensional array.
The first dimension consists of the
"records", so that in the second
dimension $AoA[$first][0] contains
the internal node references, and
$AoA[$first][1] the branching time
of the internal node, and $AoA[$first][2]
the cumulative number of lineages over
time. The records are orderered from
root to tips by time from the origin.
Returns : SCALAR[][] or FALSE
Args : NONE
Calculates the symmetric difference metric between invocant and argument. This metric is identical to the Robinson-Foulds tree comparison distance. See http://dx.doi.org/10.1016/0025-5564(81)90043-2
Type : Calculation
Title : calc_symdiff
Usage : my $symdiff =
$tree->calc_symdiff($other_tree);
Function: Returns the symmetric difference
metric between $tree and $other_tree,
sensu Penny and Hendy, 1985.
Returns : SCALAR
Args : A Bio::Phylo::Forest::Tree object
Comments: Trees in comparison must span
the same set of terminal taxa
or results are meaningless.
Calculates the Fair Proportion value for each terminal.
Type : Calculation
Title : calc_fp
Usage : my $fp = $tree->calc_fp();
Function: Returns the Fair Proportion
value for each terminal
Returns : HASHREF
Args : NONE
Calculates the Equal Splits value for each terminal
Type : Calculation Title : calc_es Usage : my $es = $tree->calc_es(); Function: Returns the Equal Splits value for each terminal Returns : HASHREF Args : NONE
Calculates the Pendant Edge value for each terminal.
Type : Calculation Title : calc_pe Usage : my $es = $tree->calc_pe(); Function: Returns the Pendant Edge value for each terminal Returns : HASHREF Args : NONE
Calculates the Shapley value for each terminal.
Type : Calculation Title : calc_shapley Usage : my $es = $tree->calc_shapley(); Function: Returns the Shapley value for each terminal Returns : HASHREF Args : NONE
The following methods are a - not entirely true-to-form - implementation of the Visitor design pattern: the nodes in a tree are visited, and rather than having an object operate on them, a set of code references is used. This can be used, for example, to serialize a tree to a string format. To create a newick string without branch lengths you would use something like this (there is a more powerful 'to_newick' method, so this is just an example):
$tree->visit_depth_first(
'-pre_daughter' => sub { print '(' },
'-post_daughter' => sub { print ')' },
'-in' => sub { print shift->get_name },
'-pre_sister' => sub { print ',' },
);
print ';';
Visits nodes depth first
Type : Visitor method
Title : visit_depth_first
Usage : $tree->visit_depth_first( -pre => sub{ ... }, -post => sub { ... } );
Function: Visits nodes in a depth first traversal, executes subs
Returns : $tree
Args : Optional handlers in the order in which they would be executed on an internal node:
# first event handler, is executed when node is reached in recursion
-pre => sub { print "pre: ", shift->get_name, "\n" },
# is executed if node has a daughter, but before that daughter is processed
-pre_daughter => sub { print "pre_daughter: ", shift->get_name, "\n" },
# is executed if node has a daughter, after daughter has been processed
-post_daughter => sub { print "post_daughter: ", shift->get_name, "\n" },
# is executed whether or not node has sisters, if it does have sisters
# they're processed first
-in => sub { print "in: ", shift->get_name, "\n" },
# is executed if node has a sister, before sister is processed
-pre_sister => sub { print "pre_sister: ", shift->get_name, "\n" },
# is executed if node has a sister, after sister is processed
-post_sister => sub { print "post_sister: ", shift->get_name, "\n" },
# is executed last
-post => sub { print "post: ", shift->get_name, "\n" },
# specifies traversal order, default 'ltr' means first_daugher -> next_sister
# traversal, alternate value 'rtl' means last_daughter -> previous_sister traversal
-order => 'ltr', # ltr = left-to-right, 'rtl' = right-to-left
Comments:
Visits nodes breadth first
Type : Visitor method
Title : visit_breadth_first
Usage : $tree->visit_breadth_first( -pre => sub{ ... }, -post => sub { ... } );
Function: Visits nodes in a breadth first traversal, executes handlers
Returns : $tree
Args : Optional handlers in the order in which they would be executed on an internal node:
# first event handler, is executed when node is reached in recursion
-pre => sub { print "pre: ", shift->get_name, "\n" },
# is executed if node has a sister, before sister is processed
-pre_sister => sub { print "pre_sister: ", shift->get_name, "\n" },
# is executed if node has a sister, after sister is processed
-post_sister => sub { print "post_sister: ", shift->get_name, "\n" },
# is executed whether or not node has sisters, if it does have sisters
# they're processed first
-in => sub { print "in: ", shift->get_name, "\n" },
# is executed if node has a daughter, but before that daughter is processed
-pre_daughter => sub { print "pre_daughter: ", shift->get_name, "\n" },
# is executed if node has a daughter, after daughter has been processed
-post_daughter => sub { print "post_daughter: ", shift->get_name, "\n" },
# is executed last
-post => sub { print "post: ", shift->get_name, "\n" },
# specifies traversal order, default 'ltr' means first_daugher -> next_sister
# traversal, alternate value 'rtl' means last_daughter -> previous_sister traversal
-order => 'ltr', # ltr = left-to-right, 'rtl' = right-to-left
Comments:
Visits nodes in a level order traversal.
Type : Visitor method
Title : visit_level_order
Usage : $tree->visit_level_order( sub{...} );
Function: Visits nodes in a level order traversal, executes sub
Returns : $tree
Args : A subroutine reference that operates on visited nodes.
Comments:
Modifies branch lengths using the mean path lengths method of Britton et al. (2002). For more about this method, see: http://dx.doi.org/10.1016/S1055-7903(02)00268-3
Type : Tree manipulator Title : chronompl Usage : $tree->chronompl; Function: Makes tree ultrametric using MPL method Returns : The modified, now ultrametric invocant. Args : NONE Comments:
Computes and assigns branch lengths using Grafen's method, which makes node ages proportional to clade size. For more about this method, see: http://dx.doi.org/10.1098/rstb.1989.0106
Type : Tree manipulator
Title : grafenbl
Usage : $tree->grafenbl;
Function: Assigns branch lengths using Grafen's method
Returns : The modified, now ultrametric invocant.
Args : Optional, a power ('rho') to which all node ages are raised
Comments:
Converts node ages to branch lengths
Type : Tree manipulator
Title : agetobl
Usage : $tree->agetobl;
Function: Converts node ages to branch lengths
Returns : The modified invocant.
Args : NONE
Comments: This method uses ages as assigned to the generic 'age' slot
on the nodes in the trees. I.e. for each node in the tree,
$node->get_generic('age') must return a number
Sets all root-to-tip path lengths equal.
Type : Tree manipulator
Title : ultrametricize
Usage : $tree->ultrametricize;
Function: Sets all root-to-tip path
lengths equal by stretching
all terminal branches to the
height of the tallest node.
Returns : The modified invocant.
Args : NONE
Comments: This method is analogous to
the 'ultrametricize' command
in Mesquite, i.e. no rate smoothing
or anything like that happens, just
a lengthening of terminal branches.
Scales the tree to the specified height.
Type : Tree manipulator
Title : scale
Usage : $tree->scale($height);
Function: Scales the tree to the
specified height.
Returns : The modified invocant.
Args : $height = a numerical value
indicating root-to-tip path length.
Comments: This method uses the
$tree->calc_tree_height method, and
so for additive trees the *average*
root-to-tip path length is scaled to
$height (i.e. some nodes might be
taller than $height, others shorter).
Randomly breaks polytomies.
Type : Tree manipulator
Title : resolve
Usage : $tree->resolve;
Function: Randomly breaks polytomies by inserting
additional internal nodes.
Returns : The modified invocant.
Args :
Comments:
Prunes argument nodes from invocant.
Type : Tree manipulator
Title : prune_tips
Usage : $tree->prune_tips(\@taxa);
Function: Prunes specified taxa from invocant.
Returns : A pruned Bio::Phylo::Forest::Tree object.
Args : A reference to an array of taxon names, or a taxa block, or a
reference to an array of taxon objects, or a reference to an
array of node objects
Comments:
Keeps argument nodes from invocant (i.e. prunes all others).
Type : Tree manipulator Title : keep_tips Usage : $tree->keep_tips(\@taxa); Function: Keeps specified taxa from invocant. Returns : The pruned Bio::Phylo::Forest::Tree object. Args : Same as prune_tips, but with inverted meaning Comments:
Converts negative branch lengths to zero.
Type : Tree manipulator
Title : negative_to_zero
Usage : $tree->negative_to_zero;
Function: Converts negative branch
lengths to zero.
Returns : The modified invocant.
Args : NONE
Comments:
Sorts nodes in ascending (or descending) order of number of children.
Type : Tree manipulator Title : ladderize Usage : $tree->ladderize(1); Function: Sorts nodes Returns : The modified invocant. Args : Optional, a true value to reverse the sort order
Sorts nodes in (an approximation of) the provided ordering. Given an array reference of taxa, an array reference of name strings or a taxa object, this method attempts to order the tips in the same way. It does this by recursively computing the rank for all internal nodes by taking the average rank of its children. This results in the following orderings:
(a,b,c,d,e,f); => $tree->sort_tips( [ qw(a c b f d e) ] ) => (a,c,b,f,d,e); (a,b,(c,d),e,f); => $tree->sort_tips( [ qw(a b e d c f) ] ); => (a,b,(e,(d,c)),f); ((a,b),((c,d),e),f); => $tree->sort_tips( [ qw(a e d c b f) ] ); => ((e,(d,c)),(a,b),f); Type : Tree manipulator Title : sort_tips Usage : $tree->sort_tips($ordering); Function: Sorts nodes Returns : The modified invocant. Args : Required, an array reference (or taxa object) whose ordering to match
Raises branch lengths to argument.
Type : Tree manipulator Title : exponentiate Usage : $tree->exponentiate($power); Function: Raises branch lengths to $power. Returns : The modified invocant. Args : A $power in any of perl's number formats.
Log argument base transform branch lengths.
Type : Tree manipulator Title : log_transform Usage : $tree->log_transform($base); Function: Log $base transforms branch lengths. Returns : The modified invocant. Args : A $base in any of perl's number formats.
Collapses internal nodes with fewer than 2 children.
Type : Tree manipulator
Title : remove_unbranched_internals
Usage : $tree->remove_unbranched_internals;
Function: Collapses internal nodes
with fewer than 2 children.
Returns : The modified invocant.
Args : NONE
Comments:
Removes all unconnected nodes.
Type : Tree manipulator Title : remove_orphans Usage : $tree->remove_orphans; Function: Removes all unconnected nodes Returns : The modified invocant. Args : NONE Comments:
Collapses one of the children of a basal bifurcation
Type : Tree manipulator Title : deroot Usage : $tree->deroot; Function: Removes root Returns : The modified invocant. Args : Optional: node to collapse Comments:
Clones invocant.
Type : Utility method
Title : clone
Usage : my $clone = $object->clone;
Function: Creates a copy of the invocant object.
Returns : A copy of the invocant.
Args : Optional: a hash of code references to
override reflection-based getter/setter copying
my $clone = $object->clone(
'set_forest' => sub {
my ( $self, $clone ) = @_;
for my $forest ( @{ $self->get_forests } ) {
$clone->set_forest( $forest );
}
},
'set_matrix' => sub {
my ( $self, $clone ) = @_;
for my $matrix ( @{ $self->get_matrices } ) {
$clone->set_matrix( $matrix );
}
);
Comments: Cloning is currently experimental, use with caution.
It works on the assumption that the output of get_foo
called on the invocant is to be provided as argument
to set_foo on the clone - such as
$clone->set_name( $self->get_name ). Sometimes this
doesn't work, for example where this symmetry doesn't
exist, or where the return value of get_foo isn't valid
input for set_foo. If such a copy fails, a warning is
emitted. To make sure all relevant attributes are copied
into the clone, additional code references can be
provided, as in the example above. Typically, this is
done by overrides of this method in child classes.
Serializes invocant to nexus string.
Type : Stringifier
Title : to_nexus
Usage : my $string = $tree->to_nexus;
Function: Turns the invocant tree object
into a nexus string
Returns : SCALAR
Args : Any arguments that can be passed to Bio::Phylo::Forest::to_nexus
Serializes invocant to newick string.
Type : Stringifier
Title : to_newick
Usage : my $string = $tree->to_newick;
Function: Turns the invocant tree object
into a newick string
Returns : SCALAR
Args : NONE
Serializes invocant to xml.
Type : Serializer Title : to_xml Usage : my $xml = $obj->to_xml; Function: Turns the invocant object into an XML string. Returns : SCALAR Args : NONE
Serializes invocant to SVG.
Type : Serializer
Title : to_svg
Usage : my $svg = $obj->to_svg;
Function: Turns the invocant object into an SVG string.
Returns : SCALAR
Args : Same args as the Bio::Phylo::Treedrawer constructor
Notes : This will only work if you have the SVG module
from CPAN installed on your system.
Type : Serializer
Title : to_dom
Usage : $tree->to_dom($dom)
Function: Generates a DOM subtree from the invocant
and its contained objects
Returns : an Element object
Args : DOM factory object
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
The Bio::Phylo::Forest::Tree object inherits from the Bio::Phylo::Listable object, so the methods defined therein also apply to trees.
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
If you use Bio::Phylo in published research, please cite it:
Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63
