Uses of Package
pal.util
Packages that use pal.util
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 that don't fit elsewhere ;^)
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 sorting etc.
Utility classes for converting PAL objects to and from XML documents.
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Classes in pal.util used by pal.algorithmics
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Classes in pal.util used by pal.alignment
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Classes in pal.util used by pal.coalescent
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Classes in pal.util used by pal.distance
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Classes in pal.util used by pal.statistics
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Classes in pal.util used by pal.substmodelClassDescriptionconstants (strings and numbers) relating to reading and writing XML.
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Classes in pal.util used by pal.supgma
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Classes in pal.util used by pal.treesearch
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ClassDescriptioninterface for an object that is comparable.interface for an object that can compare other objects for the purposes of ordering them.Interface for all objects that provide a logging facility.
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