documentation:master:graph:phylogenetictree

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Reference documentation for older polymake versions: release 3.4, release 3.3, release 3.2

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:
COPHENETIC_MATRIX

The corresponding tree distance matrix.

Type:
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


EDGE_LENGTHS

The edge lengths.

Type:

EQUIDISTANT

Checks if the input tree is equidistant.

Type:

LABELS

The labels associated to the nodes.

Type:
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


LEAVES

The indices of the taxa.

Type:

NEWICK

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

Type:
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:
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


TAXA

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

Type:
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


VISUAL

UNDOCUMENTED


  • documentation/master/graph/phylogenetictree.txt
  • Last modified: 2022/12/01 05:41
  • by 127.0.0.1