| 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 | Description |
|---|---|
| UnivariateFunction |
interface for a function of one variable
|
| Class | 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 | 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 | 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 | Description |
|---|---|
| MultivariateFunction |
interface for a function of several variables
|
| Class | 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 | Description |
|---|---|
| LMSSolver |
Title: LMSSolver
|
| Class | 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 | 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.
|