Uses of Interface pal.misc.UnitsProvider

Packages that use UnitsProvider
Package	Description
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
Modifier and Type	Class	Description
`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
Modifier and Type Class Description

class TimeOrderCharacterData
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 SUPGMATree
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`	`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
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 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