Package | Description |
---|---|
pal.distance |
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
|
pal.eval |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
|
pal.math |
Classes for math stuff such as optimisation, numerical derivatives, matrix exponentials,
random numbers, special function etc.
|
pal.mep |
Classes for the analysis of "measurably evolving populations" (mep).
|
pal.misc |
Classes that don't fit elsewhere ;^)
|
pal.substmodel |
Classes describing substitution models, i.e.
|
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).
|
pal.treesearch |
Class and Description |
---|
UnivariateFunction
interface for a function of one variable
|
Class and Description |
---|
MinimiserMonitor
interface for a classes that wish to monitor the progress of a Minimiser
|
MultivariateFunction
interface for a function of several variables
|
MultivariateMinimum
abstract base class for minimisation of a multivariate function
|
OrthogonalHints
Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum)
hints about the function that may alow it to optimise better.
|
Class and Description |
---|
LMSSolver
Title: LMSSolver
|
Matrix
Title: Matrix
|
MersenneTwisterFast
MersenneTwisterFast:
A simulation quality fast random number generator (MT19937)
with the same public methods as java.util.Random.
|
MinimiserMonitor
interface for a classes that wish to monitor the progress of a Minimiser
|
MultivariateFunction
interface for a function of several variables
|
MultivariateMinimum
abstract base class for minimisation of a multivariate function
|
MultivariateMinimum.Factory
A factory interface for MultivariateMinimums (because they aren't statefree)
|
OrderEnumerator
A means for describing odering information, and Utilities for creating such Orderings
|
OrderEnumerator.OEFactory |
OrthogonalHints
Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum)
hints about the function that may alow it to optimise better.
|
OrthogonalSearch.RoundOptimiser |
UnivariateFunction
interface for a function of one variable
|
UnivariateMinimum
minimization of a real-valued function of one variable
without using derivatives.
|
Class and Description |
---|
OrthogonalHints
Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum)
hints about the function that may alow it to optimise better.
|
Class and Description |
---|
MultivariateFunction
interface for a function of several variables
|
Class and Description |
---|
MersenneTwisterFast
MersenneTwisterFast:
A simulation quality fast random number generator (MT19937)
with the same public methods as java.util.Random.
|
OrthogonalHints
Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum)
hints about the function that may alow it to optimise better.
|
Class and Description |
---|
LMSSolver
Title: LMSSolver
|
Class and Description |
---|
OrderEnumerator
A means for describing odering information, and Utilities for creating such Orderings
|
OrthogonalHints
Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum)
hints about the function that may alow it to optimise better.
|
Class and Description |
---|
MersenneTwisterFast
MersenneTwisterFast:
A simulation quality fast random number generator (MT19937)
with the same public methods as java.util.Random.
|
MinimiserMonitor
interface for a classes that wish to monitor the progress of a Minimiser
|
MultivariateMinimum
abstract base class for minimisation of a multivariate function
|
UnivariateMinimum
minimization of a real-valued function of one variable
without using derivatives.
|