Uses of Interface
pal.misc.Units
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Packages that use Units 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). -
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Uses of Units in pal.coalescent
Classes in pal.coalescent that implement Units 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. -
Uses of Units in pal.mep
Classes in pal.mep that implement Units 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). -
Uses of Units in pal.misc
Subinterfaces of Units in pal.misc Modifier and Type Interface Description interface
UnitsProvider
interface for classes that can provide the related Units used, (asClasses in pal.misc that implement Units Modifier and Type Class Description class
TimeOrderCharacterData
Character data that expresses an order through time. -
Uses of Units in pal.supgma
Classes in pal.supgma that implement Units Modifier and Type Class Description class
SUPGMATree
constructs an SUPGMA tree from pairwise distances. -
Uses of Units in pal.tree
Subinterfaces of Units in pal.tree Modifier and Type Interface Description interface
ParameterizedTree
abstract base class for a tree with an Parameterized interfaceinterface
Tree
Interface for a phylogenetic or genealogical tree.Classes in pal.tree that implement Units 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 treesclass
SimpleTree
data structure for a binary/non-binary rooted/unrooted treesstatic class
Tree.TreeBase
class
UnconstrainedTree
provides parameter interface to an unconstrained tree (parameters are all available branch lengths)class
UPGMATree
Deprecated.Use ClusterTree
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