| Package | Description |
|---|---|
| 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.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.xml |
Utility classes for converting PAL objects to and from XML documents.
|
| Class and Description |
|---|
| SubstitutionModel
model of sequence substitution (rate matrix + rate variation).
|
| Class and Description |
|---|
| RateDistribution
abstract base class for models of rate variation over sites
employing a discrete rate distribution
|
| RateMatrix
abstract base class for all rate matrices
|
| RateMatrixGroup |
| SingleSplitDistribution |
| SubstitutionModel
model of sequence substitution (rate matrix + rate variation).
|
| Class and Description |
|---|
| SubstitutionModel
model of sequence substitution (rate matrix + rate variation).
|
| Class and Description |
|---|
| AbstractRateMatrix
abstract base class for all rate matrices
|
| AminoAcidModel
base class of rate matrices for amino acids
|
| CachedRateMatrix
a cached rate matrix.
|
| CodonModel
base class for nucleotide rate matrices
|
| GeneralREVRateMatrix
A general rate matrix class for REV style rate matrices (GTR but for all data types)
Includes the ability for arbitarily constraints
|
| MultiRateMatrixHandler |
| NeoRateMatrix
The new RateMatrix class.
|
| NucleotideModel
base class for nucleotide rate matrices
|
| RateDistribution
abstract base class for models of rate variation over sites
employing a discrete rate distribution
|
| RateMatrix
abstract base class for all rate matrices
|
| RateMatrixGroup |
| RateMatrixHandler |
| SequenceSimulator |
| SingleSplitDistribution |
| SubstitutionModel
model of sequence substitution (rate matrix + rate variation).
|
| TemporalModelChange |
| TwoStateModel
implements the most general reversible rate matrix for two-state data
|
| YangCodonModel
Yang's model of codon evolution
More advanced codon Substitution Models (of Neilson and Yang) are now included (the M1, and M2 models).
|
| YangCodonModel.SimplePositiveSelection
A Substitution Model which can be used to implment the Postitive Selection (with out continuous rate stuff)
Codon model of [1] which uses the weighted sum of a three base Codon model where
omega=0, omega=1 and omega=free
[1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene. |
| Class and Description |
|---|
| SubstitutionModel
model of sequence substitution (rate matrix + rate variation).
|
| Class and Description |
|---|
| SubstitutionModel
model of sequence substitution (rate matrix + rate variation).
|
| Class and Description |
|---|
| SubstitutionModel
model of sequence substitution (rate matrix + rate variation).
|
| Class and Description |
|---|
| RateDistribution
abstract base class for models of rate variation over sites
employing a discrete rate distribution
|
| RateMatrix
abstract base class for all rate matrices
|