Uses of Interface
pal.misc.Units
Packages that use Units
Package
Description
Classes to model population genetic processes using the coalescent.
Classes for the analysis of "measurably evolving populations" (mep).
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 Units in pal.coalescent
Classes in pal.coalescent that implement UnitsModifier and TypeClassDescriptionclass
A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.class
This class models coalescent intervals for a constant population (parameter: N0=present-day population size).class
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
This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.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).class
This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.class
This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.class
This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).class
A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.class
Skyline plot derived from a strictly bifurcating tree or a coalescent interval. -
Uses of Units in pal.mep
Modifier and TypeClassDescriptionclass
This class models a constant mutation rate (parameter: mu = mutation rate).class
This abstract class contains methods that are of general use for modelling mutation rate changes over time.class
This class models a step-wise mutation rate.class
This class models a windowed mutation rate (parameter: mu = mutation rate). -
Uses of Units in pal.misc
Modifier and TypeInterfaceDescriptioninterface
interface for classes that can provide the related Units used, (asModifier and TypeClassDescriptionclass
Character data that expresses an order through time. -
Uses of Units in pal.supgma
Classes in pal.supgma that implement UnitsModifier and TypeClassDescriptionclass
constructs an SUPGMA tree from pairwise distances. -
Uses of Units in pal.tree
Modifier and TypeInterfaceDescriptioninterface
abstract base class for a tree with an Parameterized interfaceinterface
Interface for a phylogenetic or genealogical tree.Modifier and TypeClassDescriptionclass
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 treesclass
data structure for a binary/non-binary rooted/unrooted treesstatic class
class
provides parameter interface to an unconstrained tree (parameters are all available branch lengths)class
Deprecated.Use ClusterTree