Class Summary |
ClockTree |
provides parameter interface to a clock tree
(parameters are the minimal node height differences
at each internal node) |
DatedTipsClockTree |
provides parameter interface to a clock tree with dated tips,
following A. |
Local |
Implements LOCAL (Larget and Simon, 1999) and stochastic NNI moves for unrooted trees. |
LogParameterizedTree |
This class logarithmically transforms tree parameters.
|
MutationRateModelTree |
Provides parameter interface to any clock-like tree with
serially sampled tips (parameters are the minimal node height differences
at each internal node). |
NeighborJoiningTree |
constructs a neighbor-joining tree from pairwise distances |
NodeFactory |
Creates nodes
The purpose of this class is to decouple the creation of
a class of type "Node" from its actual implementation. |
NodeUtils |
Helper routines for dealing with nodes. |
ParameterizedTree |
abstract base class for a tree with an Parameterized interface |
ReadTree |
constructs a tree reading in a New Hampshire treefile, taking care
for internal labels and branch lengths and binary/nonbinary and
rooted/unrooted trees |
RootedTreeUtils |
This class contains utility methods. |
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 |
SimulatedAlignment |
generates an artificial data set |
SplitSystem |
data structure for a set of splits |
SplitUtils |
utilities for split systems |
SUPGMATree |
constructs an SUPGMA tree from pairwise distances. |
TreeDistanceMatrix |
computes distance matrix induced by a tree
(needs only O(n^2) time, following algorithm DistanceInTree by
D.Bryant and P. |
TreeUtils |
various utility functions on trees. |
UnconstrainedTree |
provides parameter interface to an unconstrained tree
(parameters are all available branch lengths) |
UPGMATree |
constructs a UPGMA tree from pairwise distances |
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).