====== BigObject PhylogeneticTree<Scalar> ======
//from application [[..:graph|graph]]//\\
\\
 Contains a rooted phylogenetic tree (see Definition 2.2.1 from [C. Semple, M. Steel: Phylogenetics]) with edge lengths. Every edge must have a positive length. They can be defined in terms of the distance matrix and the taxa only if the distance is ultrametric; see Section 7.2 from [C. Semple, M. Steel: Phylogenetics]. The root has always index 0.

  ? Type Parameters:
  :: ''Scalar'': edge length type
  ? derived from:
  : ''[[..:graph:Graph |Graph]]''
===== Properties =====

==== no category ====
{{anchor:cophenetic_matrix:}}
  ?  **''COPHENETIC_MATRIX''**
  :: The corresponding tree distance matrix.
    ? Type:
    :''[[..:common#Matrix |Matrix]]<Scalar,[[..:common#NonSymmetric |NonSymmetric]]>''
    ? Example:
    :: The following prints the cophenetic matrix. The entries correspond to alphabetically ordered taxa.
    :: <code perl> > $T = new PhylogeneticTree(NEWICK => "(Rabbit:5,(Rat:2,Mouse:2):3):5,Wolf:10;");
 > print $T -> TAXA;
 Mouse Rabbit Rat Wolf
</code>
    :: <code perl> > print $T -> COPHENETIC_MATRIX;
 0 10 4 20
 10 0 10 20
 4 10 0 20
 20 20 20 0
</code>


----
{{anchor:edge_lengths:}}
  ?  **''EDGE_LENGTHS''**
  :: The edge lengths.
    ? Type:
    :''[[..:common#EdgeMap |EdgeMap]]<[[..:common#Undirected |Undirected]],Scalar>''


----
{{anchor:equidistant:}}
  ?  **''EQUIDISTANT''**
  :: Checks if the input tree is equidistant.
    ? Type:
    :''[[..:common#Bool |Bool]]''


----
{{anchor:labels:}}
  ?  **''LABELS''**
  :: The labels associated to the nodes.
    ? Type:
    :''[[..:common#NodeMap |NodeMap]]<[[..:common#Undirected |Undirected]],[[..:common#String |String]]>''
    ? Example:
    :: The following prints the labels of the nodes. The root is unlabeled, so an empty string is printed.
    :: <code perl> > $T = new PhylogeneticTree(NEWICK => "(Rabbit:5,(Rat:2,Mouse:2)Muroidea:3)Glires:5,Wolf:10;");
 > print $T -> LABELS;
  Glires Rabbit Muroidea Rat Mouse Wolf
</code>


----
{{anchor:leaves:}}
  ?  **''LEAVES''**
  :: The indices of the taxa.
    ? Type:
    :''[[..:common#Map |Map]]<[[..:common#String |String]],[[..:common#Int |Int]]>''


----
{{anchor:newick:}}
  ?  **''NEWICK''**
  :: A valid representation in the Newick format (see: https://evolution.genetics.washington.edu/phylip/newicktree.html).
    ? Type:
    :''[[..:common#String |String]]''
    ? Example:
    :: Prints a Newick representation of a tree given by the cophenetic matrix and its list of taxa.
    :: <code perl> > $T0 = new PhylogeneticTree(COPHENETIC_MATRIX=>[[0,10,4,20],[10,0,10,20],[4,10,0,20],[20,20,20,0]], TAXA => ["Mouse","Rabbit","Rat","Wolf"]);
 > print $T0 -> NEWICK;
 Wolf:10,(Rabbit:5,(Mouse:2,Rat:2):3):5;
</code>


----
{{anchor:node_heights:}}
  ?  **''NODE_HEIGHTS''**
  :: The distances from nodes to any of its descendant leaves.
    ? Type:
    :''[[..:common#NodeMap |NodeMap]]<[[..:common#Undirected |Undirected]],Scalar>''
    ? Example:
    :: <code perl> > $T = new PhylogeneticTree(NEWICK => "(Rabbit:5,(Rat:2,Mouse:2):3):5,Wolf:10;");
 > print rows_labeled($T -> ADJACENCY);
 0:1 6
 1:0 2 3
 2:1
 3:1 4 5
 4:3
 5:3
 6:0
</code>
    :: <code perl> > print $T -> EDGE_LENGTHS;
 5 5 3 2 2 10
</code>
    :: <code perl> > print $T -> NODE_HEIGHTS;
 10 5 0 2 0 0 0
</code>


----
{{anchor:n_taxa:}}
  ?  **''N_TAXA''**
  :: The number of taxa.
    ? Type:
    :''[[..:common#Int |Int]]''
    ? Example:
    :: The following prints the number of taxa. Note that two internal nodes are labeled; they do not count as taxa.
    :: <code perl> > $T = new PhylogeneticTree(NEWICK => "(Rabbit:5,(Rat:2,Mouse:2)Muroidea:3)Glires:5,Wolf:10;");
 > print $T -> N_TAXA;
 4
</code>


----
{{anchor:taxa:}}
  ?  **''TAXA''**
  :: The names of the taxa, i.e. the labels of the leaves.
    ? Type:
    :''[[..:common#Array |Array]]<[[..:common#String |String]]>''
    ? Example:
    :: The following prints the taxa. Note that two internal nodes are labeled; they do not count as taxa.
    :: <code perl> > $T = new PhylogeneticTree(NEWICK => "(Rabbit:5,(Rat:2,Mouse:2)Muroidea:3)Glires:5,Wolf:10;");
 > print $T -> TAXA;
 Mouse Rabbit Rat Wolf
</code>


----
===== Methods =====

==== no category ====
{{anchor:visual:}}
  ?  **''VISUAL''**
  ::UNDOCUMENTED


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