dendropy.calculate.treemeasure
: Unary Tree Statistics and Metrics¶
Statistics, metrics, measurements, and values calculated on (single) trees.

dendropy.calculate.treemeasure.
B1
(tree)[source]¶ Returns the B1 statistic: the reciprocal of the sum of the maximum number of nodes between each interior node and tip over all internal nodes excluding root.

dendropy.calculate.treemeasure.
N_bar
(tree)[source]¶ Returns the $ar{N}$ statistic: the average number of nodes above a terminal node.

dendropy.calculate.treemeasure.
colless_tree_imbalance
(tree, normalize='max')[source]¶ Returns Colless’ tree imbalance or I statistic: the sum of differences of numbers of children in left and right subtrees over all internal nodes.
normalize
specifies the normalization: “max” or True [DEFAULT]
normalized to maximum value for tree of this size
 “yule”
normalized to the Yule model
 “pda”
normalized to the PDA (Proportional to Distinguishable Arrangements) model
 None or False
no normalization

dendropy.calculate.treemeasure.
patristic_distance
(tree, taxon1, taxon2, is_bipartitions_updated=False)[source]¶ Given a tree with bipartitions encoded, and two taxa on that tree, returns the patristic distance between the two. Much more inefficient than constructing a PhylogeneticDistanceMatrix object.

dendropy.calculate.treemeasure.
pybus_harvey_gamma
(tree, prec=1e05)[source]¶ Returns the gamma statistic of Pybus and Harvey (2000). This statistic is used to test for constancy of birth and death rates over the course of a phylogeny. Under the purebirth process, the statistic should follow a standard Normal distibution: a Normal(mean=0, variance=1).
 If the lengths of different paths to the node differ by more than
prec
, then a ValueError exception will be raised indicating deviation from ultrametricty.
 Raises a Value Error if the tree is not ultrametric, is nonbinary, or has
only 2 leaves.
As a side effect a
age
attribute is added to the nodes of the tree.Pybus and Harvey. 2000. “Testing macroevolutionary models using incomplete molecular phylogenies.” Proc. Royal Society Series B: Biological Sciences. (267). 22672272
 If the lengths of different paths to the node differ by more than

dendropy.calculate.treemeasure.
sackin_index
(tree, normalize=True)[source]¶ Returns the Sackin’s index: the sum of the number of ancestors for each tip of the tree. The larger the Sackin’s index, the less balanced the tree.
normalize
specifies the normalization: True [DEFAULT]
normalized to number of leaves; this results in a value equivalent to that given by Tree.N_bar()
 “yule”
normalized to the Yule model
 “pda”
normalized to the PDA (Proportional to Distinguishable Arrangements) model
 None or False
no normalization