Uses of Package
pal.alignment

Packages that use pal.alignment
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
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
Alignment
          interface for any alignment data.
 

Classes in pal.alignment used by pal.distance
Alignment
          interface for any alignment data.
SitePattern
          takes an Alignment and determines its site patterns
 

Classes in pal.alignment used by pal.eval
Alignment
          interface for any alignment data.
SitePattern
          takes an Alignment and determines its site patterns
 

Classes in pal.alignment used by pal.popgen
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
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
AbstractAlignment
          abstract base class for any alignment data.
Alignment
          interface for any alignment data.
 

Classes in pal.alignment used by pal.treesearch
Alignment
          interface for any alignment data.
 

Classes in pal.alignment used by pal.xml
Alignment
          interface for any alignment data.