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.
|