Uses of Interface
pal.substmodel.SubstitutionModel
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Packages that use SubstitutionModel 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 -
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Uses of SubstitutionModel in pal.distance
Methods in pal.distance with parameters of type SubstitutionModel Modifier and Type Method Description static DistanceMatrix
DistanceTool. constructEvolutionaryDistances(Alignment a, SubstitutionModel sm)
Construct a distance matrix object such that the distance between sequence A, and sequence B, is the evolutionary distance by a given substitution model.static DistanceMatrixAccess
DistanceMatrixAccess.Utils. createEvolutionary(Alignment a, SubstitutionModel sm)
static DistanceMatrixGenerator
DistanceMatrixGenerator.Utils. createEvolutionary(Alignment a, SubstitutionModel sm)
static DistanceMatrixGenerator
DistanceMatrixGenerator.Utils. createParametric(Tree baseTree, SubstitutionModel sm, int numberOfSites)
Silly idea stuffvoid
AlignmentDistanceMatrix. recompute(SitePattern sp, SubstitutionModel model)
recompute maximum-likelihood distances under new site patternvoid
AlignmentDistanceMatrix. recompute(SitePattern sp, SubstitutionModel model, AlgorithmCallback callback)
recompute maximum-likelihood distances under new site patternvoid
PairwiseDistance. updateModel(SubstitutionModel m)
update model of substitutionvoid
SequencePairLikelihood. updateModel(SubstitutionModel m)
update model of substitutionConstructors in pal.distance with parameters of type SubstitutionModel Constructor Description AlignmentDistanceMatrix(SitePattern sp, SubstitutionModel m)
compute maximum-likelihood distancesAlignmentDistanceMatrix(SitePattern sp, SubstitutionModel m, AlgorithmCallback callback)
compute maximum-likelihood distancesPairwiseDistance(SitePattern sp, SubstitutionModel m)
Constructor 2 (uses evolutionary model)SequencePairLikelihood(SitePattern sp, SubstitutionModel m)
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Uses of SubstitutionModel in pal.eval
Methods in pal.eval that return SubstitutionModel Modifier and Type Method Description SubstitutionModel
LikelihoodValue. getModel()
Returns the model of this likelihood value.SubstitutionModel
SiteDetails. getRelatedModel()
Methods in pal.eval with parameters of type SubstitutionModel Modifier and Type Method Description protected abstract void
LHCalculator.AbstractExternal. calculateCategoryPatternProbabilities(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftFlatConditionalProbabilities, ConditionalProbabilityStore rightFlatConditionalProbabilities, ConditionalProbabilityStore tempStore, double[][] categoryPatternLogLikelihoodStore)
protected abstract void
LHCalculator.AbstractExternal. calculateCategoryPatternProbabilities(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, double[][] categoryPatternLikelihoodStore)
void
LHCalculator.External. calculateExtended(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore)
ConditionalProbabilityStore
LHCalculator.Internal. calculateExtended(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall)
double
LHCalculator.External. calculateLogLikelihood(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftFlatConditionalProbabilities, ConditionalProbabilityStore rightFlatConditionalProbabilities, ConditionalProbabilityStore tempStore)
Calculate the likelihood given two sub trees (left, right) and their flat (unextend) likeihood probabilitiesdouble
LHCalculator.External. calculateLogLikelihood(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilitiesstatic double
LikelihoodTool. calculateLogLikelihood(Tree tree, Alignment alignment, SubstitutionModel model)
Calculate the log likelihood of a particular set of phylogenetic datadouble
LHCalculator.External. calculateLogLikelihoodSingle(SubstitutionModel model, int[] patternWeights, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilityStore)
Calculate the likelihood given the conditional probabilites at the rootConditionalProbabilityStore
LHCalculator.Internal. calculatePostExtendedFlat(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall)
void
LHCalculator.External. calculateSingleExtendedDirect(double distance, SubstitutionModel model, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilities)
Extend the conditionals back in time by some distance, with some modelvoid
LHCalculator.External. calculateSingleExtendedIndirect(double distance, SubstitutionModel model, int numberOfPatterns, ConditionalProbabilityStore baseConditionalProbabilities, ConditionalProbabilityStore resultConditionalProbabilities)
Extend the conditionals back in time by some distance, with some modelSiteDetails
LHCalculator.AbstractExternal. calculateSiteDetailsRooted(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
SiteDetails
LHCalculator.External. calculateSiteDetailsRooted(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
Calculate the conditional probabilities of each pattern for each categorySiteDetails
LHCalculator.AbstractExternal. calculateSiteDetailsUnrooted(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftFlatConditionalProbabilities, ConditionalProbabilityStore rightFlatConditionalProbabilities, ConditionalProbabilityStore tempStore)
SiteDetails
LHCalculator.External. calculateSiteDetailsUnrooted(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore tempStore)
Calculate the conditional probabilities of each pattern for each categorystatic SiteDetails
SiteDetails.Utils. create(double[][] categoryPatternConditionalProbabilities, boolean isLoggedConditionals, SubstitutionModel model, int numberOfPatterns, int[] sitePatternMatchup, int numberOfSites, double[] siteLikelihoods)
Create a Postriors objectstatic MolecularClockLikelihoodModel.Instance
SimpleMolecularClockLikelihoodModel. createInstance(LHCalculator.Factory baseFactory, SubstitutionModel model)
static MolecularClockLikelihoodModel.Instance
SimpleMolecularClockLikelihoodModel. createInstance(SubstitutionModel model)
static UnconstrainedLikelihoodModel.Instance
SimpleUnconstrainedLikelihoodModel. createInstance(LHCalculator.Factory base, SubstitutionModel model)
Create a SimpleUnconstrainedLikelihoodModel instancestatic UnconstrainedLikelihoodModel.Instance
SimpleUnconstrainedLikelihoodModel. createInstance(LHCalculator.Generator base, SubstitutionModel model)
Create a SimpleUnconstrainedLikelihoodModel instanceConditionalProbabilityStore
LHCalculator.Leaf. getExtendedConditionalProbabilities(double distance, SubstitutionModel model, boolean modelChanged)
ConditionalProbabilityStore
SimpleLeafCalculator. getExtendedConditionalProbabilities(double distance, SubstitutionModel model, boolean modelChanged)
static Alignment
LikelihoodTool. getMatchingDataType(Alignment alignment, SubstitutionModel model)
Creates a new alignment that has a compatible data type with a substution model (needed for likelihood stuff)static double
LikelihoodOptimiser. optimiseAlternate(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits)
Optimise parameters to acheive maximum likelihood using an alternating stategy.static double
LikelihoodOptimiser. optimiseAlternate(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
Optimise parameters to acheive maximum likelihood using an alternating stategy.static Tree
LikelihoodTool. optimiseClockConstrained(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel)
Optimise the branches of a tree with regard to maximum likelihood, with a molecular clock assumption, that is, constrained such that all tips are contemporaneous, the tree is treated as rooted.static double
LikelihoodOptimiser. optimiseCombined(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits)
Optimise parameters to acheive maximum likelihood using a combined stategy.static double
LikelihoodOptimiser. optimiseCombined(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
Optimise parameters to acheive maximum likelihood using a combined stategy.static double
LikelihoodOptimiser. optimiseModel(Tree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
Optimise model parameters only to acheive maximum likelihood using a combined stategy.static Tree
LikelihoodTool. optimiseMRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateStore)
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu - one for each sampling interval.static Tree
LikelihoodTool. optimiseMRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateChangeTimes, double[] rateStore)
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu, over general time intervals.static Tree
LikelihoodTool. optimiseSRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateStore)
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and a single mutation rate parameter.static double
LikelihoodOptimiser. optimiseTree(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits)
Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy.static double
LikelihoodOptimiser. optimiseTree(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy.static Tree
LikelihoodTool. optimiseUnrooted(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel)
Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).void
LikelihoodValue. setModel(SubstitutionModel m)
define model (a site pattern must have been set before calling this method)void
GeneralLikelihoodCalculator. setup(Tree t, SubstitutionModel model)
Constructors in pal.eval with parameters of type SubstitutionModel Constructor Description GeneralLikelihoodCalculator(Alignment baseAlignment, Tree tree, SubstitutionModel model)
Constructor taking site pattern, tree and a general substitution model.InternalImpl(LHCalculator.Internal base, SubstitutionModel model)
LeafImpl(LHCalculator.Leaf base, SubstitutionModel model)
LikelihoodOptimiser(Tree tree, Alignment alignment, SubstitutionModel model)
ModelParameters(SitePattern sp, SubstitutionModel m)
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Uses of SubstitutionModel in pal.statistics
Methods in pal.statistics with parameters of type SubstitutionModel Modifier and Type Method Description static ReplicateLikelihoodEvaluator
ReplicateLikelihoodEvaluator.Utils. createRELLEvaluator(SubstitutionModel model)
Create a ReplicateLikelihoodEvaluator that based likelihood on original tree (does no optimisation)static LikelihoodEvaluator
LikelihoodEvaluator.Utils. createSimpleEvaluator(SubstitutionModel model)
Create a simple evaluator that uses UnrootedTreeSearch -
Uses of SubstitutionModel in pal.substmodel
Classes in pal.substmodel that implement SubstitutionModel Modifier and Type Class Description class
GeneralRateDistributionSubstitutionModel
class
SingleClassSubstitutionModel
static class
YangCodonModel.SimpleNeutralSelection
A Substitution Model which can be used to implment the Neutral Model (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of trwo base YangCodon models where omega=0, omega=1 repectively
[1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene.static class
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.Fields in pal.substmodel declared as SubstitutionModel Modifier and Type Field Description static SubstitutionModel
F81. JC69_MODEL
Methods in pal.substmodel that return SubstitutionModel Modifier and Type Method Description static SubstitutionModel
SubstitutionTool. createF81Model(double[] baseFrequencies)
Create an F81 model of substitutionstatic SubstitutionModel
SubstitutionTool. createF84Model(double expectedTsTv, double[] baseFrequencies)
Create an F84 model of substitutionstatic SubstitutionModel
SubstitutionTool. createGTRModel(double a, double b, double c, double d, double e, double[] baseFrequencies)
Create an GTR model of substitutionstatic SubstitutionModel
SubstitutionTool. createJC69Model()
Create a Jukes-cantor model of substitutionstatic SubstitutionModel
SubstitutionTool. createM0YangCodonModel(double kappa, double omega, double[] baseFrequencies)
Create an base Yang Codon model (M0) of substitutionstatic SubstitutionModel
SubstitutionTool. createM1YangCodonModel(double kappa, double p0, double[] baseFrequencies)
Create an neutral Yang Codon model (M1) of substitutionstatic SubstitutionModel
SubstitutionTool. createM2YangCodonModel(double kappa, double p0, double p1, double omega, double[] baseFrequencies)
Create an Positive Yang Codon model (M2) of substitutionstatic SubstitutionModel
SubstitutionModel.Utils. createSubstitutionModel(NeoRateMatrix rm, DataType dt, double[] equilibriumFrequencies)
static SubstitutionModel
SubstitutionModel.Utils. createSubstitutionModel(RateMatrix rm)
static SubstitutionModel
SubstitutionModel.Utils. createSubstitutionModel(RateMatrix rm, RateDistribution rd)
static SubstitutionModel
SubstitutionModel.Utils. createSubstitutionModel(RateMatrix rm, RateDistribution rd, boolean parameteriseDistribution)
static SubstitutionModel
SubstitutionTool. createTNModel(double kappa, double r, double[] baseFrequencies)
Create an Tamura-Nei model of substitutionSubstitutionModel
GeneralRateDistributionSubstitutionModel. getCopy()
SubstitutionModel
SingleClassSubstitutionModel. getCopy()
SubstitutionModel
YangCodonModel.SimpleNeutralSelection. getCopy()
SubstitutionModel
YangCodonModel.SimplePositiveSelection. getCopy()
Methods in pal.substmodel with parameters of type SubstitutionModel Modifier and Type Method Description static double[][][]
SubstitutionModel.Utils. generateTransitionProbabilityTables(SubstitutionModel model)
Constructors in pal.substmodel with parameters of type SubstitutionModel Constructor Description SequenceSimulator(SubstitutionModel model, int sequenceLength, boolean stochasticDistribution)
A constructor (with no provided random number generator - a fresh one is created)SequenceSimulator(SubstitutionModel model, int sequenceLength, MersenneTwisterFast random, boolean stochasticDistribution)
A constructor (with no provided random number generator - a fresh one is created) -
Uses of SubstitutionModel in pal.supgma
Methods in pal.supgma with parameters of type SubstitutionModel Modifier and Type Method Description SUPGMABase.CISummary
SUPGMABase.PopulationParameters. inferCI(AlgorithmCallback callback, int numberOfReplicates, SimulatedAlignment.Factory alignmentFactory, SubstitutionModel evolutionaryModel, LMSSolver solver)
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Uses of SubstitutionModel in pal.tree
Constructors in pal.tree with parameters of type SubstitutionModel Constructor Description Factory(int sequenceLength, SubstitutionModel model)
SimulatedAlignment(int sites, Tree t, SubstitutionModel m)
Inititalisation -
Uses of SubstitutionModel in pal.treesearch
Methods in pal.treesearch with parameters of type SubstitutionModel Modifier and Type Method Description UnrootedMLSearcher
BranchAccess. attach(java.lang.String newSequence, Alignment fullAlignment, SubstitutionModel model)
Create a new Tree Searcher with a new sub tree attachedUnrootedMLSearcher
BranchAccess. attach(Node subTree, Alignment fullAlignment, SubstitutionModel model)
Create a new Tree Searcher with a new sub tree attachedTree
TreeSearchTool. basicUnrootedTreeMLSearch(Alignment a, SubstitutionModel sm, boolean optimiseModel)
Do a basic tree search using maximum likelihood on an unrooted tree space, without a given starting treeTree
TreeSearchTool. basicUnrootedTreeMLSearch(Alignment a, SubstitutionModel sm, boolean optimiseModel, AlgorithmCallback callback)
Do a basic tree search using maximum likelihood on an unrooted tree space, without a given starting treeTree
TreeSearchTool. basicUnrootedTreeMLSearch(Tree baseTree, Alignment a, SubstitutionModel sm, boolean optimiseModel)
Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting treeTree
TreeSearchTool. basicUnrootedTreeMLSearch(Tree baseTree, Alignment a, SubstitutionModel sm, boolean optimiseModel, AlgorithmCallback callback)
Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting treestatic double
TreeSearchTool. calculateLogLikelihood(Tree tree, Alignment alignment, SubstitutionModel model)
Calculate the log likelihood of a particular set of phylogenetic datastatic Alignment
TreeSearchTool. getMatchingDataType(Alignment alignment, SubstitutionModel model)
Creates a new alignment that has a compatible data type with a substution model (needed for likelihood stuff)static Tree
TreeSearchTool. optimiseClockConstrainedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel, AlgorithmCallback callback)
Optimise the branches of a tree with regard to maximum likelihood, with the contraints of a global molecular clock - that is, all the tips terminate at the same point.static Tree
TreeSearchTool. optimiseUnrootedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel)
Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).static Tree
TreeSearchTool. optimiseUnrootedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel, AlgorithmCallback callback)
Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).Constructors in pal.treesearch with parameters of type SubstitutionModel Constructor Description UnrootedMLSearcher(Alignment alignment, SubstitutionModel model)
Build an unconstrained optimiser based on a randomly generated tree.UnrootedMLSearcher(Alignment alignment, SubstitutionModel model, LHCalculator.Factory calcFactory)
UnrootedMLSearcher(Node root, Alignment alignment, SubstitutionModel model)
UnrootedMLSearcher(Node root, Alignment alignment, SubstitutionModel model, LHCalculator.Factory calcFactory)
UnrootedMLSearcher(Node root, SubstitutionModel model)
Create a searcher based on a given tree, that has no alignment specified (useful as backbone tree for attaching new nodes)UnrootedMLSearcher(Tree t, Alignment alignment, SubstitutionModel model)
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