1.1. Introduction to Phylogenetic Data Objects

1.1.1. Types of Phylogenetic Data Objects

Phylogenetic data in DendroPy is represented by one or more objects of the following classes:

Taxon

A representation of an operational taxonomic unit, with an attribute, label, corresponding to the taxon label.

TaxonSet

A collection of Taxon objects representing a distinct definition of taxa (for example, as specified explicitly in a NEXUS “TAXA” block, or implicitly in the set of all taxon labels used across a Newick tree file).

Tree

A collection of Node and Edge objects representing a phylogenetic tree. Each Tree object maintains a reference to a TaxonSet object in its attribute, taxon_set, which specifies the set of taxa that are referenced by the tree and its nodes. Each Node object has a taxon attribute (which points to a particular Taxon object if there is an operational taxonomic unit associated with this node, or is None if not), a parent_node attribute (which will be None if the Node has no parent, e.g., a root node), a Edge attribute, as well as a list of references to child nodes, a copy of which can be obtained by calling child_nodes.

TreeList

A list of Tree objects. A TreeList object has an attribute, taxon_set, which specifies the set of taxa that are referenced by all member Tree elements. This is enforced when a Tree object is added to a TreeList, with the TaxonSet of the Tree object and all Taxon references of the Node objects in the Tree mapped to the TaxonSet of the TreeList.

CharacterMatrix

Representation of character data, with specializations for different data types: DnaCharacterMatrix, RnaCharacterMatrix, ProteinCharacterMatrix, StandardCharacterMatrix, ContinuousCharacterMatrix, etc. A CharacterMatrix can treated very much like a dict object, with Taxon objects as keys and character data as values associated with those keys.

DataSet

A meta-collection of phylogenetic data, consisting of lists of multiple TaxonSet objects (taxon_sets), TreeList objects (tree_lists), and CharacterMatrix objects (char_matrices).

1.1.2. Creating New (Empty) Objects

All of the above names are imported into the the the dendropy namespace, and so to instantiate new, empty objects of these classes, you would need to import dendropy:

>>> import dendropy
>>> tree1 = dendropy.Tree()
>>> tree_list11 = dendropy.TreeList()
>>> dna1 = dendropy.DnaCharacterMatrix()
>>> dataset1 = dendropy.DataSet()

Or import the names directly:

>>> from dendropy import Tree, TreeList, DnaCharacterMatrix, DataSet
>>> tree1 = Tree()
>>> tree_list1 = TreeList()
>>> dna1 = DnaCharacterMatrix()
>>> dataset1 = DataSet()

1.1.3. Reading and Writing Phylogenetic Data

DendroPy provides a rich set of tools for reading and writing phylogenetic data in various formats, such as NEXUS, Newick, PHYLIP, etc. These are covered in detail in the following “Reading Phylogenetic Data” and “Writing Phylogenetic Data” chapters respectively.