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.
|
Class and 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 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
|
Class and Description |
---|
Alignment
interface for any alignment data.
|
Class and Description |
---|
Alignment
interface for any alignment data.
|
SitePattern
takes an Alignment and determines its site patterns
|
Class and Description |
---|
Alignment
interface for any alignment data.
|
SitePattern
takes an Alignment and determines its site patterns
|
Class and Description |
---|
Alignment
interface for any alignment data.
|
AnnotationAlignment
The AnnotationAlignment interface is designed to provide annotation for an alignment.
|
Class and Description |
---|
Alignment
interface for any alignment data.
|
AlignmentGenerator
A AlignmentGenerator is an object that can generate alignments! (most probably replicates for statistical tests)
|
Class and Description |
---|
AbstractAlignment
abstract base class for any alignment data.
|
Alignment
interface for any alignment data.
|
Class and Description |
---|
Alignment
interface for any alignment data.
|
Class and Description |
---|
Alignment
interface for any alignment data.
|