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