Uses of Interface
pal.misc.Units

Packages that use Units
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
 

Classes in pal.coalescent that implement Units
 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
 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
 interface UnitsProvider
          interface for classes that can provide the related Units used, (as
 

Classes in pal.misc that implement Units
 class TimeOrderCharacterData
          Character data that expresses an order through time.
 

Uses of Units in pal.supgma
 

Classes in pal.supgma that implement Units
 class SUPGMATree
          constructs an SUPGMA tree from pairwise distances.
 

Uses of Units in pal.tree
 

Subinterfaces of Units in pal.tree
 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
 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