Uses of Interface
pal.misc.UnitsProvider
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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). -
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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 interfaceinterface
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 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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