Uses of Class
pal.alignment.SitePattern
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Packages that use SitePattern Package Description pal.alignment Classes dealing with sequence alignments, including methods for reading and printing in several possible formats, as well as rearranging and concatenating.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. -
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Uses of SitePattern in pal.alignment
Methods in pal.alignment that return SitePattern Modifier and Type Method Description static SitePattern
SitePattern. getSitePattern(Alignment a)
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Uses of SitePattern in pal.distance
Methods in pal.distance with parameters of type SitePattern Modifier and Type Method Description void
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
AlignmentDistanceMatrix. recompute(SitePattern sp, AlgorithmCallback callback)
recompute observed distances under new site patternvoid
PairwiseDistance. updateSitePattern(SitePattern sp)
update site patternvoid
SequencePairLikelihood. updateSitePattern(SitePattern sp)
update site patternConstructors in pal.distance with parameters of type SitePattern Constructor Description AlignmentDistanceMatrix(SitePattern sp)
compute observed distancesAlignmentDistanceMatrix(SitePattern sp, SubstitutionModel m)
compute maximum-likelihood distancesAlignmentDistanceMatrix(SitePattern sp, SubstitutionModel m, AlgorithmCallback callback)
compute maximum-likelihood distancesAlignmentDistanceMatrix(SitePattern sp, AlgorithmCallback callback)
compute observed distancesJukesCantorDistanceMatrix(SitePattern sitePattern)
compute jukes-cantor corrected distancesPairwiseDistance(SitePattern sp)
Constructor 1 (estimate observed distances only)PairwiseDistance(SitePattern sp, SubstitutionModel m)
Constructor 2 (uses evolutionary model)SequencePairLikelihood(SitePattern sp, SubstitutionModel m)
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Uses of SitePattern in pal.eval
Methods in pal.eval that return SitePattern Modifier and Type Method Description SitePattern
LikelihoodValue. getSitePattern()
Returns the site pattern of this likelihood valueSitePattern
SimpleLikelihoodCalculator. getSitePattern()
Methods in pal.eval with parameters of type SitePattern Modifier and Type Method Description void
LikelihoodValue. renewSitePattern(SitePattern sp)
Set new site pattern (while keeping tree and model)void
FastLikelihoodCalculator. updateSitePattern(SitePattern pattern)
Constructors in pal.eval with parameters of type SitePattern Constructor Description DemographicLikelihoodValue(SitePattern sp)
Parameter taking a site pattern.FastLikelihoodCalculator(SitePattern pattern)
Constructor taking only site pattern.FastLikelihoodCalculator(SitePattern pattern, Tree tree, RateMatrix model)
Constructor taking site pattern, tree and model.LikelihoodValue(SitePattern sp)
initializationModelParameters(SitePattern sp, SubstitutionModel m)
ConstructorSimpleLikelihoodCalculator(SitePattern pattern)
Need to use setTree(), and setModel() before using compute() if you use this constructorSimpleLikelihoodCalculator(SitePattern pattern, Tree tree, RateMatrix model)
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