Uses of Package
pal.misc
Packages that use pal.misc
Package
Description
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
Classes to model population genetic processes using the coalescent.
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
GUI components for some special objects (e.g., trees).
Classes for the analysis of "measurably evolving populations" (mep).
Classes that don't fit elsewhere ;^)
Classes for providing 'classical' population genetics analyses.
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.)
Classes describing substitution models, i.e.
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
Utility classes for converting PAL objects to and from XML documents.
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Classes in pal.misc used by pal.alignmentClassDescriptionAn identifier for some sampled data.An indexed group of identifiers.interface for classes that can print out a human readable report of itselfinterface for classes with data that can be presented in tables
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Classes in pal.misc used by pal.coalescentClassDescriptionAn indexed group of identifiers.interface for class with (optimizable) parametersinterface for classes that can print out a human readable report of itselfinterface for classes that can provide summariesCharacter data that expresses an order through time.interface holding unit constantsinterface for classes that can provide the related Units used, (as
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Classes in pal.misc used by pal.distanceClassDescriptionAn identifier for some sampled data.An indexed group of identifiers.
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ClassDescriptioninterface for class with (optimizable) parameters.An event used by PalObjectListenersDefines objects that monitor certain PalObjects for changesinterface for class with (optimizable) parametersCharacter data that expresses an order through time.
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ClassDescriptionAn identifier for some sampled data.Character data that expresses an order through time.
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ClassDescriptionDefines objects that monitor certain PalObjects for changesinterface for class with (optimizable) parametersinterface for classes that can print out a human readable report of itselfTitle: SampleInformationinterface for classes that can provide summariesCharacter data that expresses an order through time.interface holding unit constants
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ClassDescriptionlimits for branch lengthsDefines objects that listen to exteneral ParameterEventsAn identifier for some sampled data.An indexed group of identifiers.Title:An interface for classes that wish to find out about particular parameter accessinterface for classes that can be named.interface for class with (optimizable) parameters.An event used by PalObjectListenersDefines objects that monitor certain PalObjects for changesA base class for classes that fire PalObject eventsAn event used by ExternalParameterListenersinterface for class with (optimizable) parametersTitle: SampleInformationinterface for classes that can provide summariesCharacter data that expresses an order through time.interface holding unit constantsinterface for classes that can provide the related Units used, (as
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Classes in pal.misc used by pal.popgen
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Classes in pal.misc used by pal.statistics
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Classes in pal.misc used by pal.substmodelClassDescriptionDefines objects that listen to exteneral ParameterEventsinterface for class with (optimizable) named parametersinterface for class with (optimizable) parameters.An event used by PalObjectListenersDefines objects that monitor certain PalObjects for changesA base class for classes that fire PalObject eventsAn event used by ExternalParameterListenersinterface for class with (optimizable) parametersA Utility class for using as the superclass to subclasses which work by adding functionality to a general Parameterized object (the base Parameterized object)interface for classes that can print out a human readable report of itselfCharacter data that expresses an order through time.
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Classes in pal.misc used by pal.supgmaClassDescriptionAn indexed group of identifiers.interface for classes that can print out a human readable report of itselfCharacter data that expresses an order through time.interface holding unit constantsinterface for classes that can provide the related Units used, (as
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ClassDescriptionAn identifier for some sampled data.An indexed group of identifiers.interface for class with (optimizable) parametersinterface for classes that can print out a human readable report of itselfCharacter data that expresses an order through time.interface holding unit constantsinterface for classes that can provide the related Units used, (as
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Classes in pal.misc used by pal.treesearchClassDescriptioninterface for class with (optimizable) parameters.Title: SampleInformation
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ClassDescriptionAn immutable attribute has a name and value.An identifier for some sampled data.Character data that expresses an order through time.