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Packages that use Units | |
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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). |
Uses of Units in pal.coalescent |
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Classes in pal.coalescent that implement Units | |
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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. |
Uses of Units in pal.mep |
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Classes in pal.mep that implement Units | |
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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). |
Uses of Units in pal.misc |
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Subinterfaces of Units in pal.misc | |
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interface |
UnitsProvider
interface for classes that can provide the related Units used, (as |
Classes in pal.misc that implement Units | |
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class |
TimeOrderCharacterData
Character data that expresses an order through time. |
Uses of Units in pal.supgma |
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Classes in pal.supgma that implement Units | |
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class |
SUPGMATree
constructs an SUPGMA tree from pairwise distances. |
Uses of Units in pal.tree |
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Subinterfaces of Units in pal.tree | |
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interface |
ParameterizedTree
abstract base class for a tree with an Parameterized interface |
interface |
Tree
Interface for a phylogenetic or genealogical tree. |
Classes in pal.tree that implement Units | |
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class |
ClockTree
provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node) |
class |
ClusterTree
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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
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class |
UnconstrainedTree
provides parameter interface to an unconstrained tree (parameters are all available branch lengths) |
class |
UPGMATree
Deprecated. Use ClusterTree |
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