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Bio::Tree::Compatible(User Contributed Perl DocumentatBio::Tree::Compatible(3)

NAME
       Bio::Tree::Compatible - Testing compatibility of	phylogenetic trees
       with nested taxa.

SYNOPSIS
	 use Bio::Tree::Compatible;
	 use Bio::TreeIO;
	 my $input = Bio::TreeIO->new('-format'	=> 'newick',
				      '-file'	=> 'input.tre');
	 my $t1	= $input->next_tree;
	 my $t2	= $input->next_tree;

	 my ($incompat,	$ilabels, $inodes) = Bio::Tree::Compatible::is_compatible($t1,$t2);
	 if ($incompat)	{
	   my %cluster1	= %{ Bio::Tree::Compatible::cluster_representation($t1)	};
	   my %cluster2	= %{ Bio::Tree::Compatible::cluster_representation($t2)	};
	   print "incompatible trees\n";
	   if (scalar(@$ilabels)) {
	     foreach my	$label (@$ilabels) {
	       my $node1 = $t1->find_node(-id => $label);
	       my $node2 = $t2->find_node(-id => $label);
	       my @c1 =	sort @{	$cluster1{$node1} };
	       my @c2 =	sort @{	$cluster2{$node2} };
	       print "label $label";
	       print " cluster"; map { print " ",$_ } @c1;
	       print " cluster"; map { print " ",$_ } @c2; print "\n";
	     }
	   }
	   if (scalar(@$inodes)) {
	     while (@$inodes) {
	       my $node1 = shift @$inodes;
	       my $node2 = shift @$inodes;
	       my @c1 =	sort @{	$cluster1{$node1} };
	       my @c2 =	sort @{	$cluster2{$node2} };
	       print "cluster";	map { print " ",$_ } @c1;
	       print " properly	intersects cluster";
	       map { print " ",$_ } @c2; print "\n";
	     }
	   }
	 } else	{
	   print "compatible trees\n";
	 }

DESCRIPTION
       NB: This	module has exclusively class methods that work on
       Bio::Tree::TreeI	objects. An instance of	Bio::Tree::Compatible cannot
       itself represent	a tree,	and so typically there is no need to create
       one.

       Bio::Tree::Compatible is	a Perl tool for	testing	compatibility of
       phylogenetic trees with nested taxa represented as Bio::Tree::Tree
       objects.	It is based on a recent	characterization of ancestral
       compatibility of	semi-labeled trees in terms of their cluster
       representations.

       A semi-labeled tree is a	phylogenetic tree with some of its internal
       nodes labeled, and it can represent a classification tree as well as a
       phylogenetic tree with nested taxa, with	labeled	internal nodes
       corresponding to	taxa at	a higher level of aggregation or nesting than
       that of their descendents.

       Two semi-labeled	trees are compatible if	their topological restrictions
       to the common labels are	such that for each node	label, the smallest
       clusters	containing it in each of the trees coincide and, furthermore,
       no cluster in one of the	trees properly intersects a cluster of the
       other tree.

       Future extensions of Bio::Tree::Compatible include a
       Bio::Tree::Supertree module for combining compatible phylogenetic trees
       with nested taxa	into a common supertree.

FEEDBACK
   Mailing Lists
       User feedback is	an integral part of the	evolution of this and other
       Bioperl modules.	Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About	the mailing lists

   Support
       Please direct usage questions or	support	issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and
       reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the	problem	with code and
       data examples if	at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of
       the bugs	and their resolution. Bug reports can be submitted via the
       web:

	 https://github.com/bioperl/bioperl-live/issues

SEE ALSO
       o   Philip Daniel and Charles Semple. Supertree Algorithms for Nested
	   Taxa. In: Olaf R. P.	Bininda-Emonds (ed.) Phylogenetic Supertrees:
	   Combining Information to Reveal the Tree of Life, Computational
	   Biology, vol. 4, chap. 7, pp. 151-171. Kluwer (2004).

       o   Charles Semple, Philip Daniel, Wim Hordijk, Roderic D. M. Page, and
	   Mike	Steel: Supertree Algorithms for	Ancestral Divergence Dates and
	   Nested Taxa.	Bioinformatics 20(15), 2355-2360 (2004).

       o   Merce Llabres, Jairo	Rocha, Francesc	Rossello, and Gabriel
	   Valiente: On	the Ancestral Compatibility of Two Phylogenetic	Trees
	   with	Nested Taxa. J.	Math. Biol. 53(3), 340-364 (2006).

AUTHOR - Gabriel Valiente
       Email valiente@lsi.upc.edu

APPENDIX
       The rest	of the documentation details each of the object	methods.

   postorder_traversal
	Title	: postorder_traversal
	Usage	: my @nodes = @{ $tree->postorder_traversal }
	Function: Return list of nodes in postorder
	Returns	: reference to array of	Bio::Tree::Node
	Args	: none

       For example, the	postorder traversal of the tree
       "(((A,B)C,D),(E,F,G));" is a reference to an array of nodes with
       internal_id 0 through 9,	because	the Newick standard representation for
       phylogenetic trees is based on a	postorder traversal.

		 +---A			  +---0
		 |			  |
	 +---+---C		  +---4---2
	 |   |	 |		  |   |	  |
	 |   |	 +---B		  |   |	  +---1
	 |   |			  |   |
	 +   +-------D		  9   +-------3
	 |			  |
	 |     +-----E		  |	+-----5
	 |     |		  |	|
	 +-----+-----F		  +-----8-----6
	       |			|
	       +-----G			+-----7

   cluster_representation
	Title	: cluster_representation
	Usage	: my %cluster =	%{ $tree->cluster_representation }
	Function: Compute the cluster representation of	a tree
	Returns	: reference to hash of array of	string indexed by
		  Bio::Tree::Node
	Args	: none

       For example, the	cluster	representation of the tree
       "(((A,B)C,D),(E,F,G));" is a reference to a hash	associating an array
       of string (descendent labels) to	each node, as follows:

	 0 --> [A]
	 1 --> [B]
	 2 --> [A,B,C]
	 3 --> [D]
	 4 --> [A,B,C,D]
	 5 --> [E]
	 6 --> [F]
	 7 --> [G]
	 8 --> [E,F,G]
	 9 --> [A,B,C,D,E,F,G]

   common_labels
	Title	: common_labels
	Usage	: my $labels = $tree1->common_labels($tree2);
	Function: Return set of	common node labels
	Returns	: Set::Scalar
	Args	: Bio::Tree::Tree

       For example, the	common labels of the tree "(((A,B)C,D),(E,F,G));" and
       the tree	"((A,B)H,E,(J,(K)G)I);"	are: "[A,B,E,G]".

		 +---A		       +---A
		 |		       |
	 +---+---C	       +-------H
	 |   |	 |	       |       |
	 |   |	 +---B	       |       +---B
	 |   |		       |
	 +   +-------D	       +-----------E
	 |		       |
	 |     +-----E	       |   +-------J
	 |     |	       |   |
	 +-----+-----F	       +---I
	       |		   |
	       +-----G		   +---G---K

   topological_restriction
	Title	: topological_restriction
	Usage	: $tree->topological_restriction($labels)
	Function: Compute the topological restriction of a tree	to a subset
		  of node labels
	Returns	: Bio::Tree::Tree
	Args	: Set::Scalar

       For example, the	topological restrictions of each of the	trees
       "(((A,B)C,D),(E,F,G));" and "((A,B)H,E,(J,(K)G)I);" to the labels
       "[A,B,E,G]" are as follows:

		 +---A		   +---A
		 |		   |
	 +---+---+	       +---+
	 |	 |	       |   |
	 |	 +---B	       |   +---B
	 +		       |
	 |	 +---E	       +-------E
	 |	 |	       |
	 +-------+	       +---+---G
		 |
		 +---G

   is_compatible
	Title	: is_compatible
	Usage	: $tree1->is_compatible($tree2)
	Function: Test compatibility of	two trees
	Returns	: boolean
	Args	: Bio::Tree::Tree

       For example, the	topological restrictions of the	trees
       "(((A,B)C,D),(E,F,G));" and "((A,B)H,E,(J,(K)G)I);" to their common
       labels, "[A,B,E,G]", are	compatible. The	respective cluster
       representations are as follows:

	 [A]		      [A]
	 [B]		      [B]
	 [E]		      [E]
	 [G]		      [G]
	 [A,B]		      [A,B]
	 [E,G]		      [A,B,E,G]
	 [A,B,E,G]

       As a second example, the	trees "(A,B);" and "((B)A);" are incompatible.
       Their respective	cluster	representations	are as follows:

	 [A]		      [B]
	 [B]		      [A,B]
	 [A,B]

       The reason is, the smallest cluster containing label "A"	is "[A]" in
       the first tree but "[A,B]" in the second	tree.

	+---A	      A---B
	|
	+
	|
	+---B

       As a second example, the	trees "(((B,A),C),D);" and "((A,(D,B)),C);"
       are also	incompatible. Their respective cluster representations are as
       follows:

	 [A]		      [A]
	 [B]		      [B]
	 [C]		      [C]
	 [D]		      [D]
	 [A,B]		      [B,D]
	 [A,B,C]	      [A,B,D]
	 [A,B,C,D]	      [A,B,C,D]

       The reason is, cluster "[A,B]" properly intersects cluster "[B,D]".
       There are further incompatibilities between these trees:	"[A,B,C]"
       properly	intersects both	"[B,D]"	and "[A,B,D]".

		 +---B		   +-------A
		 |		   |
	     +---+	       +---+   +---D
	     |	 |	       |   |   |
	 +---+	 +---A	       |   +---+
	 |   |		       +       |
	 +   +-------C	       |       +---B
	 |		       |
	 +-----------D	       +-----------C

perl v5.24.1			  2017-07-08	      Bio::Tree::Compatible(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | SEE ALSO | AUTHOR - Gabriel Valiente | APPENDIX

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