Uses of Interface
org.forester.evoinference.matrix.distance.DistanceMatrix
Packages that use DistanceMatrix
Package
Description
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Uses of DistanceMatrix in org.biojava.nbio.phylo
Methods in org.biojava.nbio.phylo that return DistanceMatrixModifier and TypeMethodDescriptionstatic <C extends Sequence<D>,
D extends Compound>
DistanceMatrixDistanceMatrixCalculator.dissimilarityScore
(MultipleSequenceAlignment<C, D> msa, SubstitutionMatrix<D> M) The dissimilarity score is the additive inverse of the similarity score (sum of scores) between two aligned sequences using a substitution model (Substitution Matrix).static <C extends Sequence<D>,
D extends Compound>
DistanceMatrixDistanceMatrixCalculator.fractionalDissimilarity
(MultipleSequenceAlignment<C, D> msa) The fractional dissimilarity (D) is defined as the percentage of sites that differ between two aligned sequences.static <C extends Sequence<D>,
D extends Compound>
DistanceMatrixDistanceMatrixCalculator.fractionalDissimilarityScore
(MultipleSequenceAlignment<C, D> msa, SubstitutionMatrix<D> M) The fractional dissimilarity score (Ds) is a relative measure of the dissimilarity between two aligned sequences.static <C extends Sequence<D>,
D extends Compound>
DistanceMatrixDistanceMatrixCalculator.kimuraDistance
(MultipleSequenceAlignment<C, D> msa) The Kimura evolutionary distance (d) is a correction of the fractional dissimilarity (D) specially needed for large evolutionary distances.static <C extends Sequence<D>,
D extends Compound>
DistanceMatrixDistanceMatrixCalculator.pamMLdistance
(MultipleSequenceAlignment<C, D> msa) The PAM (Point Accepted Mutations) distance is a measure of evolutionary distance in protein sequences.static <C extends Sequence<D>,
D extends Compound>
DistanceMatrixDistanceMatrixCalculator.percentageIdentity
(MultipleSequenceAlignment<C, D> msa) BioJava implementation for percentage of identity (PID).static <C extends Sequence<D>,
D extends Compound>
DistanceMatrixDistanceMatrixCalculator.poissonDistance
(MultipleSequenceAlignment<C, D> msa) The Poisson (correction) evolutionary distance (d) is a function of the fractional dissimilarity (D), given by:static <C extends Sequence<D>,
D extends Compound>
DistanceMatrixDistanceMatrixCalculator.structuralDistance
(double[][] rmsdMat, double alpha, double rmsdMax, double rmsd0) The structural distance (dS) uses the structural similarity (or dissimilarity) from a the structural alignment of two protein strutures.Methods in org.biojava.nbio.phylo with parameters of type DistanceMatrixModifier and TypeMethodDescriptionstatic double
DistanceTreeEvaluator.evaluate
(Phylogeny tree, DistanceMatrix matrix) Evaluate the goodness of fit of a given tree to the original distance matrix. -
Uses of DistanceMatrix in org.forester.evoinference.matrix.distance
Classes in org.forester.evoinference.matrix.distance that implement DistanceMatrix -
Uses of DistanceMatrix in org.forester.io.parsers
Methods in org.forester.io.parsers that return DistanceMatrixModifier and TypeMethodDescription -
Uses of DistanceMatrix in org.forester.surfacing
Methods in org.forester.surfacing that return types with arguments of type DistanceMatrixModifier and TypeMethodDescriptionPairwiseGenomeComparator.getDomainDistanceScoresMeans()
PairwiseGenomeComparator.getSharedBinaryCombinationsBasedDistances()
PairwiseGenomeComparator.getSharedDomainsBasedDistances()
Methods in org.forester.surfacing with parameters of type DistanceMatrixModifier and TypeMethodDescriptionstatic Phylogeny
SurfacingUtil.createNjTreeBasedOnMatrixToFile
(File nj_tree_outfile, DistanceMatrix distance) Method parameters in org.forester.surfacing with type arguments of type DistanceMatrixModifier and TypeMethodDescriptionstatic void
SurfacingUtil.writeMatrixToFile
(File matrix_outfile, List<DistanceMatrix> matrices)