static <C extends Sequence<D>,D extends Compound> org.forester.msa.Msa |
ForesterWrapper.convert(MultipleSequenceAlignment<C,D> msa) |
|
static <C extends Sequence<D>,D extends Compound> org.forester.evoinference.matrix.distance.DistanceMatrix |
DistanceMatrixCalculator.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> org.forester.evoinference.matrix.distance.DistanceMatrix |
DistanceMatrixCalculator.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> org.forester.evoinference.matrix.distance.DistanceMatrix |
DistanceMatrixCalculator.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> org.forester.evoinference.matrix.distance.DistanceMatrix |
DistanceMatrixCalculator.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> org.forester.evoinference.matrix.distance.DistanceMatrix |
DistanceMatrixCalculator.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> org.forester.evoinference.matrix.distance.DistanceMatrix |
DistanceMatrixCalculator.percentageIdentity(MultipleSequenceAlignment<C,D> msa) |
BioJava implementation for percentage of identity (PID).
|
static <C extends Sequence<D>,D extends Compound> org.forester.evoinference.matrix.distance.DistanceMatrix |
DistanceMatrixCalculator.poissonDistance(MultipleSequenceAlignment<C,D> msa) |
The Poisson (correction) evolutionary distance (d) is a function of the
fractional dissimilarity (D), given by:
|