Uses of Class
pal.alignment.SitePattern
Packages that use SitePattern
Package
Description
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
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.
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Uses of SitePattern in pal.alignment
Methods in pal.alignment that return SitePatternModifier and TypeMethodDescriptionstatic final SitePattern
SitePattern.getSitePattern
(Alignment a) -
Uses of SitePattern in pal.distance
Methods in pal.distance with parameters of type SitePatternModifier and TypeMethodDescriptionvoid
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 SitePatternModifierConstructorDescriptioncompute observed distancescompute 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 distancesConstructor 1 (estimate observed distances only)Constructor 2 (uses evolutionary model)initialisation -
Uses of SitePattern in pal.eval
Methods in pal.eval that return SitePatternModifier and TypeMethodDescriptionLikelihoodValue.getSitePattern()
Returns the site pattern of this likelihood valueSimpleLikelihoodCalculator.getSitePattern()
Methods in pal.eval with parameters of type SitePatternModifier and TypeMethodDescriptionvoid
LikelihoodValue.renewSitePattern
(SitePattern sp) Set new site pattern (while keeping tree and model)final void
FastLikelihoodCalculator.updateSitePattern
(SitePattern pattern) Constructors in pal.eval with parameters of type SitePatternModifierConstructorDescriptionParameter 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.initializationConstructorSimpleLikelihoodCalculator
(SitePattern pattern) Need to use setTree(), and setModel() before using compute() if you use this constructorSimpleLikelihoodCalculator
(SitePattern pattern, Tree tree, RateMatrix model)