Package | Description |
---|---|
pal.alignment |
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
|
pal.coalescent |
Classes to model population genetic processes using the coalescent.
|
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.gui |
GUI components for some special objects (e.g., trees).
|
pal.mep |
Classes for the analysis of "measurably evolving populations" (mep).
|
pal.misc |
Classes that don't fit elsewhere ;^)
|
pal.popgen |
Classes for providing 'classical' population genetics analyses.
|
pal.statistics |
Classes with useful for statistics (normal distribution,
Gamma distribution, chi-square distribution, exponential distribution,
likelihood-ratio test, chi-square test, descriptive statistics, bootstrap estimators etc.)
|
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 | |
pal.xml |
Utility classes for converting PAL objects to and from XML documents.
|
Class | Description |
---|---|
Identifier |
An identifier for some sampled data.
|
IdGroup |
An indexed group of identifiers.
|
LabelMapping | |
Report |
interface for classes that can print out a human readable report of itself
|
TableReport |
interface for classes with data that can be presented in tables
|
Class | Description |
---|---|
IdGroup |
An indexed group of identifiers.
|
Parameterized |
interface for class with (optimizable) parameters
|
Report |
interface for classes that can print out a human readable report of itself
|
Summarizable |
interface for classes that can provide summaries
|
TimeOrderCharacterData |
Character data that expresses an order through time.
|
Units |
interface holding unit constants
|
UnitsProvider |
interface for classes that can provide the related Units used, (as
|
Class | Description |
---|---|
Identifier |
An identifier for some sampled data.
|
IdGroup |
An indexed group of identifiers.
|
Class | Description |
---|---|
NeoParameterized |
interface for class with (optimizable) parameters.
|
PalObjectEvent |
An event used by PalObjectListeners
|
PalObjectListener |
Defines objects that monitor certain PalObjects for changes
|
Parameterized |
interface for class with (optimizable) parameters
|
TimeOrderCharacterData |
Character data that expresses an order through time.
|
Class | Description |
---|---|
Identifier |
An identifier for some sampled data.
|
LabelMapping | |
TimeOrderCharacterData |
Character data that expresses an order through time.
|
Class | Description |
---|---|
PalObjectListener |
Defines objects that monitor certain PalObjects for changes
|
Parameterized |
interface for class with (optimizable) parameters
|
Report |
interface for classes that can print out a human readable report of itself
|
SampleInformation |
Title: SampleInformation
|
Summarizable |
interface for classes that can provide summaries
|
TimeOrderCharacterData |
Character data that expresses an order through time.
|
Units |
interface holding unit constants
|
Class | Description |
---|---|
BranchLimits |
limits for branch lengths
|
ExternalParameterListener |
Defines objects that listen to exteneral ParameterEvents
|
Identifier |
An identifier for some sampled data.
|
IdGroup |
An indexed group of identifiers.
|
IndividualParameterHandler |
Title:
|
IndividualParameterHandler.Listener | |
LabelMapping | |
LabelMapping.Relabeller | |
MultiParameterized.ParameterAccessWatcher |
An interface for classes that wish to find out about particular parameter access
|
MutableDouble | |
Nameable |
interface for classes that can be named.
|
NeoParameterized |
interface for class with (optimizable) parameters.
|
PalObjectEvent |
An event used by PalObjectListeners
|
PalObjectListener |
Defines objects that monitor certain PalObjects for changes
|
PalObjectListener.EventGenerator |
A base class for classes that fire PalObject events
|
ParameterEvent |
An event used by ExternalParameterListeners
|
Parameterized |
interface for class with (optimizable) parameters
|
SampleInformation |
Title: SampleInformation
|
Summarizable |
interface for classes that can provide summaries
|
TimeOrderCharacterData |
Character data that expresses an order through time.
|
Units |
interface holding unit constants
|
UnitsProvider |
interface for classes that can provide the related Units used, (as
|
Class | Description |
---|---|
TableReport |
interface for classes with data that can be presented in tables
|
Class | Description |
---|---|
Report |
interface for classes that can print out a human readable report of itself
|
Class | Description |
---|---|
ExternalParameterListener |
Defines objects that listen to exteneral ParameterEvents
|
MutableDouble | |
NamedParameterized |
interface for class with (optimizable) named parameters
|
NeoParameterized |
interface for class with (optimizable) parameters.
|
PalObjectEvent |
An event used by PalObjectListeners
|
PalObjectListener |
Defines objects that monitor certain PalObjects for changes
|
PalObjectListener.EventGenerator |
A base class for classes that fire PalObject events
|
ParameterEvent |
An event used by ExternalParameterListeners
|
Parameterized |
interface for class with (optimizable) parameters
|
Parameterized.ParameterizedUser |
A Utility class for using as the superclass to subclasses which work by adding functionality to
a general Parameterized object (the base Parameterized object)
|
Report |
interface for classes that can print out a human readable report of itself
|
TimeOrderCharacterData |
Character data that expresses an order through time.
|
Class | Description |
---|---|
IdGroup |
An indexed group of identifiers.
|
Report |
interface for classes that can print out a human readable report of itself
|
TimeOrderCharacterData |
Character data that expresses an order through time.
|
Units |
interface holding unit constants
|
UnitsProvider |
interface for classes that can provide the related Units used, (as
|
Class | Description |
---|---|
Identifier |
An identifier for some sampled data.
|
IdGroup |
An indexed group of identifiers.
|
LabelMapping | |
Parameterized |
interface for class with (optimizable) parameters
|
Report |
interface for classes that can print out a human readable report of itself
|
TimeOrderCharacterData |
Character data that expresses an order through time.
|
Units |
interface holding unit constants
|
UnitsProvider |
interface for classes that can provide the related Units used, (as
|
Class | Description |
---|---|
NeoParameterized |
interface for class with (optimizable) parameters.
|
SampleInformation |
Title: SampleInformation
|
Class | Description |
---|---|
Attribute |
An immutable attribute has a name and value.
|
Identifier |
An identifier for some sampled data.
|
TimeOrderCharacterData |
Character data that expresses an order through time.
|