Uses of Package
pal.substmodel
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Packages that use pal.substmodel 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. -
Classes in pal.substmodel used by pal.distance Class Description SubstitutionModel model of sequence substitution (rate matrix + rate variation). -
Classes in pal.substmodel used by pal.eval Class Description RateDistribution abstract base class for models of rate variation over sites employing a discrete rate distributionRateMatrix abstract base class for all rate matricesRateMatrixGroup SingleSplitDistribution SubstitutionModel model of sequence substitution (rate matrix + rate variation). -
Classes in pal.substmodel used by pal.statistics Class Description SubstitutionModel model of sequence substitution (rate matrix + rate variation). -
Classes in pal.substmodel used by pal.substmodel Class Description AbstractRateMatrix abstract base class for all rate matricesAminoAcidModel base class of rate matrices for amino acidsCachedRateMatrix a cached rate matrix.CodonModel base class for nucleotide rate matricesGeneralREVRateMatrix A general rate matrix class for REV style rate matrices (GTR but for all data types) Includes the ability for arbitarily constraintsMultiRateMatrixHandler NeoRateMatrix The new RateMatrix class.NucleotideModel base class for nucleotide rate matricesRateDistribution abstract base class for models of rate variation over sites employing a discrete rate distributionRateMatrix abstract base class for all rate matricesRateMatrixGroup RateMatrixHandler SequenceSimulator SingleSplitDistribution SubstitutionModel model of sequence substitution (rate matrix + rate variation).TemporalModelChange TwoStateModel implements the most general reversible rate matrix for two-state dataYangCodonModel 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 Class Description SubstitutionModel model of sequence substitution (rate matrix + rate variation). -
Classes in pal.substmodel used by pal.tree Class Description SubstitutionModel model of sequence substitution (rate matrix + rate variation). -
Classes in pal.substmodel used by pal.treesearch Class Description SubstitutionModel model of sequence substitution (rate matrix + rate variation). -
Classes in pal.substmodel used by pal.xml Class Description RateDistribution abstract base class for models of rate variation over sites employing a discrete rate distributionRateMatrix abstract base class for all rate matrices