Uses of Package
pal.alignment

Packages that use pal.alignment

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.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.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.

Classes in pal.alignment used by pal.alignment

Class and Description
AbstractAlignment abstract base class for any alignment data.
Alignment interface for any alignment data.
AlignmentGenerator A AlignmentGenerator is an object that can generate alignments! (most probably replicates for statistical tests)
AlignmentParseException Exception thrown by ReadAlignment
AlignmentReceiver
AnnotationAlignment The AnnotationAlignment interface is designed to provide annotation for an alignment.
CharacterAlignment This interface is designed to hold quantitative character states.
IndelAlignment This class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms.
SimpleAlignment An alignment class that can be efficiently constructed from an array of strings.
SitePattern takes an Alignment and determines its site patterns
StrippedAlignment takes an alignment and repeatedly removes sites

Classes in pal.alignment used by pal.coalescent

Class and Description
Alignment interface for any alignment data.

Classes in pal.alignment used by pal.distance

Class and Description
Alignment interface for any alignment data.
SitePattern takes an Alignment and determines its site patterns

Classes in pal.alignment used by pal.eval

Class and Description
Alignment interface for any alignment data.
SitePattern takes an Alignment and determines its site patterns

Classes in pal.alignment used by pal.popgen

Class and Description
Alignment interface for any alignment data.
AnnotationAlignment The AnnotationAlignment interface is designed to provide annotation for an alignment.

Classes in pal.alignment used by pal.statistics

Class and Description
Alignment interface for any alignment data.
AlignmentGenerator A AlignmentGenerator is an object that can generate alignments! (most probably replicates for statistical tests)

Classes in pal.alignment used by pal.tree

Class and Description
AbstractAlignment abstract base class for any alignment data.
Alignment interface for any alignment data.

Classes in pal.alignment used by pal.treesearch

Class and Description
Alignment interface for any alignment data.

Classes in pal.alignment used by pal.xml

Class and Description
Alignment interface for any alignment data.