Modules and data types

Phylo package

The Phylo package provides some simple phylogenetics types (e.g. NamedTree) to interface to the Diversity package for measuring phylogenetic diversity. It also provides an interface to R for copying trees to and from that language and can read newick and nexus tree files (including TreeSets that contain multiple trees).

Finally it also provides a standard abstract interface to phylogenetic trees, by defining AbstractNode, AbstractBranch and AbstractTree supertypes, and methods to interface to them. It also provides (through the Phylo.API submodule) methods to (re)define to write your own phylogenetic type in a way that will interact cleanly with other phylogenetic packages.

TreeSet

A collection of trees with the same tips.

struct RecoursiveTree <: AbstractTree

A phylogenetic tree type containing RecursiveElts as both nodes and branches, allowing navigation of the tree using only the node and branch elements.

struct LinkTree <: AbstractTree

A phylogenetic tree type containing LinkNodes and LinkBranches

NamedBinaryTree

Binary phylogenetic tree object with known leaves

BinaryTree

Binary phylogenetic tree object with known leaves and per node data

NamedPolytomousTree

Polytomous phylogenetic tree object with known leaves

PolytomousTree

Phylogenetic tree object with polytomous branching, and known leaves and per node data

PolytomousTree

Phylogenetic tree object with polytomous branching, and known leaves and per node data

struct RecursiveElt <: AbstractElt

A type for branches or nodes in a RecursiveTree, allowing navigation of the tree without using the tree object itself.

struct LinkNode <: AbstractNode

A node type that is connected by LinkBranches in a LinkTree

struct BinaryNode <: AbstractNode

A node of strict binary phylogenetic tree

struct Node <: AbstractNode

A node of potentially polytomous phylogenetic tree

struct LinkBranch <: AbstractBranch

A branch type that connects LinkNodes in a LinkTree

Branch

A branch connecting two AbstractNodes of a phylogenetic tree

BranchIterator

The struct representing an iterator for branches of a phylogenetic tree

BranchNameIterator

The struct representing an iterator for branchnames of a phylogenetic tree

NodeIterator

The struct representing an iterator for nodes of a phylogenetic tree

NodeNameIterator

The struct representing an iterator for nodenames of a phylogenetic tree