Uses of Package
pal.alignment
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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 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 ReadAlignmentAlignmentReceiver 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 patternsStrippedAlignment takes an alignment and repeatedly removes sites -
Classes in pal.alignment used by pal.coalescent Class Description Alignment interface for any alignment data. -
Classes in pal.alignment used by pal.distance Class 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 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 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 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 Description AbstractAlignment abstract base class for any alignment data.Alignment interface for any alignment data. -
Classes in pal.alignment used by pal.treesearch Class Description Alignment interface for any alignment data. -
Classes in pal.alignment used by pal.xml Class Description Alignment interface for any alignment data.