Uses of Package
pal.substmodel

Packages that use pal.substmodel

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.

Classes in pal.substmodel used by pal.distance

SubstitutionModel
model of sequence substitution (rate matrix + rate variation).

Classes in pal.substmodel used by pal.eval

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).

Classes in pal.substmodel used by pal.statistics

SubstitutionModel
model of sequence substitution (rate matrix + rate variation).

Classes in pal.substmodel used by pal.substmodel

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.

Classes in pal.substmodel used by pal.supgma

SubstitutionModel
model of sequence substitution (rate matrix + rate variation).

Classes in pal.substmodel used by pal.tree

SubstitutionModel
model of sequence substitution (rate matrix + rate variation).

Classes in pal.substmodel used by pal.treesearch

SubstitutionModel
model of sequence substitution (rate matrix + rate variation).

Classes in pal.substmodel used by pal.xml

RateDistribution
abstract base class for models of rate variation over sites employing a discrete rate distribution

RateMatrix
abstract base class for all rate matrices