| Interface | Description |
|---|---|
| AttributeNode |
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree. Unlike its superclass this node can have an arbitrary number of named attributes associated with it.
|
| BranchLimits |
limits for branch lengths
|
| Node |
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree
|
| Parameterized |
interface for class with (optimizable) parameters
|
| Tree |
Interface for a phylogenetic or genealogical tree.
|
| Units |
interface holding unit constants
|
| UnitsProvider |
interface for classes that can provide the related Units used, (as
|
| Class | Description |
|---|---|
| CladeSystem |
data structure for a set of splits
|
| LabelMapping | |
| MultiParameterized |
Title: MultiParameterized
|
| NeighborJoiningTree |
constructs a neighbor-joining tree from pairwise distances
Saitou, N., and Nei, M., (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol, 4(4):406-425, |
| NewickUtils | |
| NodeFactory | |
| NodeUtils |
Helper routines for dealing with nodes.
|
| RootedTreeUtils |
This class contains utility methods. These include:
1. gathering information about subtrees from a set of trees 2. comparing subtrees and clades. All these methods assume rooted trees! |
| SimpleNode |
data structure for a node (includes branch) in a binary/non-binary rooted/unrooted tree
|
| SimpleTree |
data structure for a binary/non-binary rooted/unrooted trees
|
| SplitSystem |
data structure for a set of splits
|
| SplitUtils |
utilities for split systems
|
| TreeClusters | |
| TreeUtils |
various utility functions on trees.
|
| UPGMATree |
constructs a UPGMA tree from pairwise distances
|
| Exception | Description |
|---|---|
| TreeParseException |
exception thrown by ReadTree
|