Package | Description |
---|---|
pal.coalescent |
Classes to model population genetic processes using the coalescent.
|
pal.misc |
Classes that don't fit elsewhere ;^)
|
pal.supgma | |
pal.tree |
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
|
Modifier and Type | Class | Description |
---|---|---|
class |
DemographicClockTree |
Provides parameter interface to a clock-like genealogy which is
assumed to have some demographic pattern of theta (diversity) as
well as branch parameters (the minimal node height differences
at each internal node).
|
Modifier and Type | Class | Description |
---|---|---|
class |
TimeOrderCharacterData |
Character data that expresses an order through time.
|
Modifier and Type | Class | Description |
---|---|---|
class |
SUPGMATree |
constructs an SUPGMA tree from pairwise distances.
|
Modifier and Type | Interface | Description |
---|---|---|
interface |
ParameterizedTree |
abstract base class for a tree with an Parameterized interface
|
interface |
Tree |
Interface for a phylogenetic or genealogical tree.
|
Modifier and Type | Class | Description |
---|---|---|
class |
ClockTree |
provides parameter interface to a clock tree
(parameters are the minimal node height differences
at each internal node)
|
class |
ClusterTree |
|
class |
LogParameterizedTree |
This class logarithmically transforms tree parameters.
|
class |
MutationRateModelTree |
Provides parameter interface to any clock-like tree with
serially sampled tips (parameters are the minimal node height differences
at each internal node).
|
class |
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. |
static class |
ParameterizedTree.ParameterizedTreeBase |
For parameterisations that work by adjusting a base tree (that is, they aren't really
tree's themselves...)
|
class |
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
|
class |
SimpleTree |
data structure for a binary/non-binary rooted/unrooted trees
|
static class |
Tree.TreeBase |
|
class |
UnconstrainedTree |
provides parameter interface to an unconstrained tree
(parameters are all available branch lengths)
|
class |
UPGMATree |
Deprecated.
Use ClusterTree
|