Uses of Class
org.biojava.nbio.core.sequence.MultipleSequenceAlignment

Packages that use MultipleSequenceAlignment

Package	Description
org.biojava.nbio.phylo
org.biojava.nbio.structure.align.multiple.util

Uses of MultipleSequenceAlignment in org.biojava.nbio.phylo

Methods in org.biojava.nbio.phylo with parameters of type MultipleSequenceAlignment

Modifier and Type	Method and Description
static <C extends Sequence<D>,D extends Compound> org.forester.msa.Msa	ForesterWrapper.convert(MultipleSequenceAlignment<C,D> msa) Convert a BioJava MultipleSequenceAlignment to a forester 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: d = -log(1 - D) The gapped positons in the alignment are ignored in the calculation.

Uses of MultipleSequenceAlignment in org.biojava.nbio.structure.align.multiple.util

Methods in org.biojava.nbio.structure.align.multiple.util that return MultipleSequenceAlignment

Modifier and Type	Method and Description
static MultipleSequenceAlignment<ProteinSequence,AminoAcidCompound>	MultipleAlignmentTools.toProteinMSA(MultipleAlignment msta) Convert a MultipleAlignment into a MultipleSequenceAlignment of AminoAcid residues.