Uses of Interface
pal.misc.UnitsProvider

Packages that use UnitsProvider
Package
Description
Classes to model population genetic processes using the coalescent.
Classes that don't fit elsewhere ;^)
 
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
    Modifier and Type
    Class
    Description
    class 
    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
    Modifier and Type
    Class
    Description
    class 
    Character data that expresses an order through time.
  • Uses of UnitsProvider in pal.supgma

    Classes in pal.supgma that implement UnitsProvider
    Modifier and Type
    Class
    Description
    class 
    constructs an SUPGMA tree from pairwise distances.
  • Uses of UnitsProvider in pal.tree

    Subinterfaces of UnitsProvider in pal.tree
    Modifier and Type
    Interface
    Description
    interface 
    abstract base class for a tree with an Parameterized interface
    interface 
    Interface for a phylogenetic or genealogical tree.
    Classes in pal.tree that implement UnitsProvider
    Modifier and Type
    Class
    Description
    class 
    provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)
    class 
     
    class 
    This class logarithmically transforms tree parameters.
    class 
    Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).
    class 
    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 
    For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)
    class 
    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 
    data structure for a binary/non-binary rooted/unrooted trees
    static class 
     
    class 
    provides parameter interface to an unconstrained tree (parameters are all available branch lengths)
    class 
    Deprecated.
    Use ClusterTree