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 | Description |
---|---|
SubstitutionModel |
model of sequence substitution (rate matrix + rate variation).
|
Class | 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 | Description |
---|---|
SubstitutionModel |
model of sequence substitution (rate matrix + rate variation).
|
Class | 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 | Description |
---|---|
SubstitutionModel |
model of sequence substitution (rate matrix + rate variation).
|
Class | Description |
---|---|
SubstitutionModel |
model of sequence substitution (rate matrix + rate variation).
|
Class | Description |
---|---|
SubstitutionModel |
model of sequence substitution (rate matrix + rate variation).
|
Class | 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
|