Uses of Package
pal.substmodel
Packages that use pal.substmodel
Package
Description
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
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.)
Classes describing substitution models, i.e.
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
Utility classes for converting PAL objects to and from XML documents.
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Classes in pal.substmodel used by pal.distance
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Classes in pal.substmodel used by pal.evalClassDescriptionabstract base class for models of rate variation over sites employing a discrete rate distributionabstract base class for all rate matricesmodel of sequence substitution (rate matrix + rate variation).
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Classes in pal.substmodel used by pal.statistics
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Classes in pal.substmodel used by pal.substmodelClassDescriptionabstract base class for all rate matricesbase class of rate matrices for amino acidsa cached rate matrix.base class for nucleotide rate matricesA general rate matrix class for REV style rate matrices (GTR but for all data types) Includes the ability for arbitarily constraintsThe new RateMatrix class.base class for nucleotide rate matricesabstract base class for models of rate variation over sites employing a discrete rate distributionabstract base class for all rate matricesmodel of sequence substitution (rate matrix + rate variation).implements the most general reversible rate matrix for two-state dataYang's model of codon evolution More advanced codon Substitution Models (of Neilson and Yang) are now included (the M1, and M2 models).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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Classes in pal.substmodel used by pal.tree
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Classes in pal.substmodel used by pal.treesearch
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Classes in pal.substmodel used by pal.xmlClassDescriptionabstract base class for models of rate variation over sites employing a discrete rate distributionabstract base class for all rate matrices