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Packages that use SitePattern | |
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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. |
Uses of SitePattern in pal.alignment |
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Methods in pal.alignment that return SitePattern | |
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static SitePattern |
SitePattern.getSitePattern(Alignment a)
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Uses of SitePattern in pal.distance |
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Methods in pal.distance with parameters of type SitePattern | |
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void |
AlignmentDistanceMatrix.recompute(SitePattern sp,
AlgorithmCallback callback)
recompute observed distances under new site pattern |
void |
AlignmentDistanceMatrix.recompute(SitePattern sp,
SubstitutionModel model)
recompute maximum-likelihood distances under new site pattern |
void |
AlignmentDistanceMatrix.recompute(SitePattern sp,
SubstitutionModel model,
AlgorithmCallback callback)
recompute maximum-likelihood distances under new site pattern |
void |
SequencePairLikelihood.updateSitePattern(SitePattern sp)
update site pattern |
void |
PairwiseDistance.updateSitePattern(SitePattern sp)
update site pattern |
Constructors in pal.distance with parameters of type SitePattern | |
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AlignmentDistanceMatrix(SitePattern sp)
compute observed distances |
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AlignmentDistanceMatrix(SitePattern sp,
AlgorithmCallback callback)
compute observed distances |
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AlignmentDistanceMatrix(SitePattern sp,
SubstitutionModel m)
compute maximum-likelihood distances |
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AlignmentDistanceMatrix(SitePattern sp,
SubstitutionModel m,
AlgorithmCallback callback)
compute maximum-likelihood distances |
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JukesCantorDistanceMatrix(SitePattern sitePattern)
compute jukes-cantor corrected distances |
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PairwiseDistance(SitePattern sp)
Constructor 1 (estimate observed distances only) |
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PairwiseDistance(SitePattern sp,
SubstitutionModel m)
Constructor 2 (uses evolutionary model) |
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SequencePairLikelihood(SitePattern sp,
SubstitutionModel m)
initialisation |
Uses of SitePattern in pal.eval |
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Methods in pal.eval that return SitePattern | |
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SitePattern |
SimpleLikelihoodCalculator.getSitePattern()
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SitePattern |
LikelihoodValue.getSitePattern()
Returns the site pattern of this likelihood value |
Methods in pal.eval with parameters of type SitePattern | |
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void |
LikelihoodValue.renewSitePattern(SitePattern sp)
Set new site pattern (while keeping tree and model) |
void |
FastLikelihoodCalculator.updateSitePattern(SitePattern pattern)
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Constructors in pal.eval with parameters of type SitePattern | |
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DemographicLikelihoodValue(SitePattern sp)
Parameter taking a site pattern. |
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FastLikelihoodCalculator(SitePattern pattern)
Constructor taking only site pattern. |
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FastLikelihoodCalculator(SitePattern pattern,
Tree tree,
RateMatrix model)
Constructor taking site pattern, tree and model. |
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LikelihoodValue(SitePattern sp)
initialization |
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ModelParameters(SitePattern sp,
SubstitutionModel m)
Constructor |
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SimpleLikelihoodCalculator(SitePattern pattern)
Need to use setTree(), and setModel() before using compute() if you use this constructor |
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SimpleLikelihoodCalculator(SitePattern pattern,
Tree tree,
RateMatrix model)
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