Uses of Package
pal.alignment
Packages that use pal.alignment
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.
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 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.alignment used by pal.alignmentClassDescriptionabstract base class for any alignment data.interface for any alignment data.A AlignmentGenerator is an object that can generate alignments! (most probably replicates for statistical tests)Exception thrown by ReadAlignmentThe AnnotationAlignment interface is designed to provide annotation for an alignment.This interface is designed to hold quantitative character states.This class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms.An alignment class that can be efficiently constructed from an array of strings.takes an Alignment and determines its site patternstakes an alignment and repeatedly removes sites
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Classes in pal.alignment used by pal.coalescent
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Classes in pal.alignment used by pal.distanceClassDescriptioninterface for any alignment data.takes an Alignment and determines its site patterns
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Classes in pal.alignment used by pal.evalClassDescriptioninterface for any alignment data.takes an Alignment and determines its site patterns
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Classes in pal.alignment used by pal.popgenClassDescriptioninterface for any alignment data.The AnnotationAlignment interface is designed to provide annotation for an alignment.
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Classes in pal.alignment used by pal.statisticsClassDescriptioninterface for any alignment data.A AlignmentGenerator is an object that can generate alignments! (most probably replicates for statistical tests)
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Classes in pal.alignment used by pal.treeClassDescriptionabstract base class for any alignment data.interface for any alignment data.
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Classes in pal.alignment used by pal.treesearch
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Classes in pal.alignment used by pal.xml