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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:

	 http://bugzilla.open-bio.org/

SEE ALSO
       ·   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).

       ·   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).

       ·   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 v5.14.1			  2011-07-22	      Bio::Tree::Compatible(3)
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