BigObject PhylogeneticTree<Scalar>

from application 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

COPHENETIC_MATRIX

The corresponding tree distance matrix.

Type:

Matrix<Scalar,NonSymmetric>

Example:

The following prints the cophenetic matrix. The entries correspond to alphabetically ordered taxa.

 > $T = new PhylogeneticTree(NEWICK => "(Rabbit:5,(Rat:2,Mouse:2):3):5,Wolf:10;");
 > print $T -> TAXA;
 Mouse Rabbit Rat Wolf

 > print $T -> COPHENETIC_MATRIX;
 0 10 4 20
 10 0 10 20
 4 10 0 20
 20 20 20 0

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EDGE_LENGTHS

The edge lengths.

Type:

EdgeMap<Undirected,Scalar>

---

EQUIDISTANT

Checks if the input tree is equidistant.

Type:

Bool

---

LABELS

The labels associated to the nodes.

Type:

NodeMap<Undirected,String>

Example:

The following prints the labels of the nodes. The root is unlabeled, so an empty string is printed.

 > $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

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LEAVES

The indices of the taxa.

Type:

Map<String,Int>

---

NEWICK

A valid representation in the Newick format (see: https://evolution.genetics.washington.edu/phylip/newicktree.html).

Type:

String

Example:

Prints a Newick representation of a tree given by the cophenetic matrix and its list of taxa.

 > $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;

---

NODE_HEIGHTS

The distances from nodes to any of its descendant leaves.

Type:

NodeMap<Undirected,Scalar>

Example:

 > $T = new PhylogeneticTree(NEWICK => "(Rabbit:5,(Rat:2,Mouse:2):3):5,Wolf:10;");
 > print rows_labeled($T -> ADJACENCY);
 0:1 6
 1:0 2 3
 2:1
 3:1 4 5
 4:3
 5:3
 6:0

 > print $T -> EDGE_LENGTHS;
 5 5 3 2 2 10

 > print $T -> NODE_HEIGHTS;
 10 5 0 2 0 0 0

---

N_TAXA

The number of taxa.

Type:

Int

Example:

The following prints the number of taxa. Note that two internal nodes are labeled; they do not count as taxa.

 > $T = new PhylogeneticTree(NEWICK => "(Rabbit:5,(Rat:2,Mouse:2)Muroidea:3)Glires:5,Wolf:10;");
 > print $T -> N_TAXA;
 4

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TAXA

The names of the taxa, i.e. the labels of the leaves.

Type:

Array<String>

Example:

The following prints the taxa. Note that two internal nodes are labeled; they do not count as taxa.

 > $T = new PhylogeneticTree(NEWICK => "(Rabbit:5,(Rat:2,Mouse:2)Muroidea:3)Glires:5,Wolf:10;");
 > print $T -> TAXA;
 Mouse Rabbit Rat Wolf

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VISUAL

UNDOCUMENTED

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