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