| Package | Description |
|---|---|
| pal.algorithmics | |
| 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.misc |
Classes that don't fit elsewhere ;^)
|
| 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.substmodel |
Classes describing substitution models, i.e.
|
| pal.supgma | |
| 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.util |
Utility classes for sorting etc.
|
| pal.xml |
Utility classes for converting PAL objects to and from XML documents.
|
| Class and Description |
|---|
| AlgorithmCallback |
| Class and Description |
|---|
| AlgorithmCallback |
| Class and Description |
|---|
| AlgorithmCallback |
| Class and Description |
|---|
| AlgorithmCallback |
| Class and Description |
|---|
| Comparable
interface for an object that is comparable.
|
| Class and Description |
|---|
| AlgorithmCallback |
| Class and Description |
|---|
| DoubleKeyCache |
| XMLConstants
constants (strings and numbers) relating to reading and writing XML.
|
| Class and Description |
|---|
| AlgorithmCallback |
| Class and Description |
|---|
| AlgorithmCallback |
| Class and Description |
|---|
| AlgorithmCallback |
| Class and Description |
|---|
| AlgorithmCallback |
| Comparable
interface for an object that is comparable.
|
| Comparator
interface for an object that can compare other objects for the
purposes of ordering them.
|
| DoubleKey |
| DoubleKeyCache |
| Logger
Interface for all objects that provide a logging facility.
|
| Class and Description |
|---|
| XMLConstants
constants (strings and numbers) relating to reading and writing XML.
|