

o  Philip Daniel and Charles Semple. Supertree Algorithms for Nested Taxa. In: Olaf R. P. BinindaEmonds (ed.) Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, Computational Biology, vol. 4, chap. 7, pp. 151171. 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 <B>20B>(15), 23552360 (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. <B>53B>(3), 340364 (2006). 
Email valiente@lsi.upc.edu
The rest of the documentation details each of the object methods.
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 : noneFor 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 +42         +B   +1     + +D 9 +3    +E  +5     ++F +86   +G +7
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 : noneFor 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]
Title : common_labels Usage : my $labels = $tree1>common_labels($tree2); Function: Return set of common node labels Returns : Set::Scalar Args : Bio::Tree::TreeFor 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 +GK
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::ScalarFor 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
Title : is_compatible Usage : $tree1>is_compatible($tree2) Function: Test compatibility of two trees Returns : boolean Args : Bio::Tree::TreeFor 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 AB  +  +BAs 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 v5.20.3  BIO::TREE::COMPATIBLE (3)  20160405 
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