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Packages that use pal.substmodel | |
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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 | |
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SubstitutionModel
model of sequence substitution (rate matrix + rate variation). |
Classes in pal.substmodel used by pal.eval | |
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RateDistribution
abstract base class for models of rate variation over sites employing a discrete rate distribution |
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RateMatrix
abstract base class for all rate matrices |
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RateMatrixGroup
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SingleSplitDistribution
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SubstitutionModel
model of sequence substitution (rate matrix + rate variation). |
Classes in pal.substmodel used by pal.statistics | |
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SubstitutionModel
model of sequence substitution (rate matrix + rate variation). |
Classes in pal.substmodel used by pal.substmodel | |
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AbstractRateMatrix
abstract base class for all rate matrices |
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AminoAcidModel
base class of rate matrices for amino acids |
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CachedRateMatrix
a cached rate matrix. |
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CodonModel
base class for nucleotide rate matrices |
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GeneralREVRateMatrix
A general rate matrix class for REV style rate matrices (GTR but for all data types) Includes the ability for arbitarily constraints |
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MultiRateMatrixHandler
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NeoRateMatrix
The new RateMatrix class. |
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NucleotideModel
base class for nucleotide rate matrices |
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RateDistribution
abstract base class for models of rate variation over sites employing a discrete rate distribution |
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RateMatrix
abstract base class for all rate matrices |
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RateMatrixGroup
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RateMatrixHandler
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SequenceSimulator
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SingleSplitDistribution
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SubstitutionModel
model of sequence substitution (rate matrix + rate variation). |
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TemporalModelChange
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TwoStateModel
implements the most general reversible rate matrix for two-state data |
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YangCodonModel
Yang's model of codon evolution More advanced codon Substitution Models (of Neilson and Yang) are now included (the M1, and M2 models). |
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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 | |
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SubstitutionModel
model of sequence substitution (rate matrix + rate variation). |
Classes in pal.substmodel used by pal.tree | |
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SubstitutionModel
model of sequence substitution (rate matrix + rate variation). |
Classes in pal.substmodel used by pal.treesearch | |
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SubstitutionModel
model of sequence substitution (rate matrix + rate variation). |
Classes in pal.substmodel used by pal.xml | |
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RateDistribution
abstract base class for models of rate variation over sites employing a discrete rate distribution |
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RateMatrix
abstract base class for all rate matrices |
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