Uses of Interface
org.forester.msa.Msa
Packages that use Msa
Package
Description
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Uses of Msa in org.biojava.nbio.phylo
Methods in org.biojava.nbio.phylo that return MsaModifier and TypeMethodDescriptionForesterWrapper.convert(MultipleSequenceAlignment<C, D> msa) Convert a BioJavaMultipleSequenceAlignmentto a foresterMsa. -
Uses of Msa in org.forester.archaeopteryx
Methods in org.forester.archaeopteryx that return Msa -
Uses of Msa in org.forester.archaeopteryx.tools
Constructors in org.forester.archaeopteryx.tools with parameters of type MsaModifierConstructorDescriptionPhylogeneticInferrer(Msa msa, PhylogeneticInferenceOptions options, MainFrameApplication mf) -
Uses of Msa in org.forester.development
Constructors in org.forester.development with parameters of type Msa -
Uses of Msa in org.forester.evoinference.distance
Methods in org.forester.evoinference.distance with parameters of type MsaModifier and TypeMethodDescriptionPairwiseDistanceCalculator.calcFractionalDissimilarities(Msa msa) PairwiseDistanceCalculator.calcKimuraDistances(Msa msa) PairwiseDistanceCalculator.calcKimuraDistances(Msa msa, double value_for_too_large_distance_for_kimura_formula) PairwiseDistanceCalculator.calcPoissonDistances(Msa msa) -
Uses of Msa in org.forester.evoinference.tools
Methods in org.forester.evoinference.tools that return MsaMethods in org.forester.evoinference.tools with parameters of type Msa -
Uses of Msa in org.forester.io.parsers
Methods in org.forester.io.parsers that return Msa -
Uses of Msa in org.forester.msa
Classes in org.forester.msa that implement MsaModifier and TypeClassDescriptionclassfinal classfinal classMethods in org.forester.msa that return MsaModifier and TypeMethodDescriptionstatic MsaBasicMsa.createInstance(List<MolecularSequence> seqs) final MsaMsaMethods.deleteGapColumns(double max_allowed_gap_ratio, int min_allowed_length, Msa msa) ClustalOmega.infer(List<MolecularSequence> seqs, List<String> opts) Mafft.infer(List<MolecularSequence> seqs, List<String> opts) abstract Msaabstract MsaMsaInferrer.infer(List<MolecularSequence> seqs, List<String> opts) static final MsaMsaMethods.removeSequence(Msa msa, String to_remove_id) static final MsaMsaMethods.removeSequences(Msa msa, List<String> to_remove_ids) static MsaMsaMethods.removeSequencesByMinimalLength(Msa msa, int min_effective_length) static final MsaMsaMethods.removeSequencesByRow(Msa msa, List<Integer> to_remove_rows) Methods in org.forester.msa with parameters of type MsaModifier and TypeMethodDescriptionstatic DescriptiveStatisticsMsaMethods.calcBasicGapinessStatistics(Msa msa) static doubleMsaMethods.calcGapRatio(Msa msa) static intDeleteableMsa.calcGapSumPerColumn(Msa msa, int col) static intMsaMethods.calcGapSumPerColumn(Msa msa, int col) static final doubleMsaMethods.calcNormalizedShannonsEntropy(int k, Msa msa) static final doubleMsaMethods.calcNormalizedShannonsEntropy(int k, Msa msa, int col) static final int[]MsaMethods.calcNumberOfGapsInMsa(Msa msa) static final DescriptiveStatisticsMsaMethods.calcNumberOfGapsStats(Msa msa) static final DescriptiveStatisticsMsaMethods.calculateEffectiveLengthStatistics(Msa msa) static final DescriptiveStatisticsMsaMethods.calculateIdentityRatio(int from, int to, Msa msa) static final doubleMsaMethods.calculateIdentityRatio(Msa msa, int column) MsaMethods.calculateResidueDestributionPerColumn(Msa msa, int column) static final DeleteableMsaDeleteableMsa.createInstance(Msa msa) final MsaMsaMethods.deleteGapColumns(double max_allowed_gap_ratio, int min_allowed_length, Msa msa) static final MsaMsaMethods.removeSequence(Msa msa, String to_remove_id) static final MsaMsaMethods.removeSequences(Msa msa, List<String> to_remove_ids) static MsaMsaMethods.removeSequencesByMinimalLength(Msa msa, int min_effective_length) static final MsaMsaMethods.removeSequencesByRow(Msa msa, List<Integer> to_remove_rows) -
Uses of Msa in org.forester.msa_compactor
Methods in org.forester.msa_compactor that return MsaConstructors in org.forester.msa_compactor with parameters of type MsaModifierConstructorDescriptionMsaProperties(Msa msa, String removed_seq, boolean calculate_normalized_shannon_entropy) -
Uses of Msa in org.forester.phylogeny
Methods in org.forester.phylogeny with parameters of type MsaModifier and TypeMethodDescriptionstatic voidPhylogenyMethods.addMolecularSeqsToTree(Phylogeny phy, Msa msa)