| 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.
|