Uses of Interface
pal.misc.UnitsProvider

Packages that use UnitsProvider
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). 
 

Uses of UnitsProvider in pal.coalescent
 

Classes in pal.coalescent that implement UnitsProvider
 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).
 

Uses of UnitsProvider in pal.misc
 

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

Uses of UnitsProvider in pal.supgma
 

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

Uses of UnitsProvider in pal.tree
 

Subinterfaces of UnitsProvider 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 UnitsProvider
 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