Package | Description |
---|---|
pal.coalescent |
Classes to model population genetic processes using the coalescent.
|
pal.mep |
Classes for the analysis of "measurably evolving populations" (mep).
|
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 |
CoalescentIntervals |
A series of coalescent intervals representing the time
order information contained in a (serial) clock-constrained
tree.
|
class |
ConstantPopulation |
This class models coalescent intervals for a constant population
(parameter: N0=present-day population size).
|
class |
ConstExpConst |
This class models a population that grows exponentially from an
initial population size alpha N0 at time y to a size N0
at time x until the present-day.
|
class |
ConstExpGrowth |
This class models a population that grows
exponentially from an inital population size alpha N0 to a present-day size N0.
|
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).
|
class |
DemographicModel |
This abstract class contains methods that are of general use for
modelling coalescent intervals given a demographic model.
|
class |
ExpandingPopulation |
This class models a population that grows
exponentially from an inital population size alpha N0 to a present-day size N0.
|
class |
ExponentialGrowth |
This class models an exponentially growing (or shrinking) population
(Parameters: N0=present-day population size; r=growth rate).
|
class |
IntervalsExtractor |
A series of coalescent intervals representing the time
order information contained in a (serial) clock-constrained
tree.
|
class |
SkylinePlot |
Skyline plot derived from a strictly bifurcating tree
or a coalescent interval.
|
Modifier and Type | Class | Description |
---|---|---|
class |
ConstantMutationRate |
This class models a constant mutation rate
(parameter: mu = mutation rate).
|
class |
MutationRateModel |
This abstract class contains methods that are of general use for
modelling mutation rate changes over time.
|
class |
SteppedMutationRate |
This class models a step-wise mutation rate.
|
class |
WindowedMutationRate |
This class models a windowed mutation rate
(parameter: mu = mutation rate).
|
Modifier and Type | Interface | Description |
---|---|---|
interface |
UnitsProvider |
interface for classes that can provide the related Units used, (as
|
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
|