Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W _ __bool__() (skbio.alignment.TabularMSA method) (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) __call__() (skbio.alignment.StripedSmithWaterman method) (skbio.workflow.method method) (skbio.workflow.requires method) (skbio.workflow.Workflow method) __contains__() (skbio.alignment.TabularMSA method) (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) __copy__() (skbio.alignment.TabularMSA method) (skbio.metadata.IntervalMetadata method) (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.tree.TreeNode method) __deepcopy__() (skbio.alignment.TabularMSA method) (skbio.metadata.IntervalMetadata method) (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.tree.TreeNode method) __delete__() (skbio.util.classproperty method) __eq__() (skbio.alignment.AlignmentStructure method) (skbio.alignment.AlignPath method) (skbio.alignment.PairAlignPath method) (skbio.alignment.StripedSmithWaterman method) (skbio.alignment.TabularMSA method) (skbio.embedding.Embedding method) (skbio.embedding.ProteinEmbedding method) (skbio.embedding.ProteinVector method) (skbio.embedding.SequenceEmbedding method) (skbio.embedding.SequenceVector method) (skbio.io.registry.Format method) (skbio.io.registry.IORegistry method) (skbio.metadata.CategoricalMetadataColumn method) (skbio.metadata.Interval method) (skbio.metadata.IntervalMetadata method) (skbio.metadata.MetadataColumn method) (skbio.metadata.NumericMetadataColumn method) (skbio.metadata.SampleMetadata method) (skbio.sequence.DNA method) (skbio.sequence.GeneticCode method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) (skbio.stats.gradient.AverageGradientANOVA method) (skbio.stats.gradient.CategoryResults method) (skbio.stats.gradient.FirstDifferenceGradientANOVA method) (skbio.stats.gradient.GradientANOVA method) (skbio.stats.gradient.GradientANOVAResults method) (skbio.stats.gradient.GroupResults method) (skbio.stats.gradient.TrajectoryGradientANOVA method) (skbio.stats.gradient.WindowDifferenceGradientANOVA method) (skbio.stats.ordination.OrdinationResults method) (skbio.table.Table method) (skbio.tree.TreeNode method) (skbio.util.classproperty method) (skbio.workflow.method method) (skbio.workflow.requires method) (skbio.workflow.Workflow method) __ge__() (skbio.alignment.AlignmentStructure method) (skbio.alignment.AlignPath method) (skbio.alignment.PairAlignPath method) (skbio.alignment.StripedSmithWaterman method) (skbio.alignment.TabularMSA method) (skbio.embedding.Embedding method) (skbio.embedding.ProteinEmbedding method) (skbio.embedding.ProteinVector method) (skbio.embedding.SequenceEmbedding method) (skbio.embedding.SequenceVector method) (skbio.io.registry.Format method) (skbio.io.registry.IORegistry method) (skbio.metadata.CategoricalMetadataColumn method) (skbio.metadata.Interval method) (skbio.metadata.IntervalMetadata method) (skbio.metadata.MetadataColumn method) (skbio.metadata.NumericMetadataColumn method) (skbio.metadata.SampleMetadata method) (skbio.sequence.DNA method) (skbio.sequence.GeneticCode method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) (skbio.stats.gradient.AverageGradientANOVA method) (skbio.stats.gradient.CategoryResults method) (skbio.stats.gradient.FirstDifferenceGradientANOVA method) (skbio.stats.gradient.GradientANOVA method) (skbio.stats.gradient.GradientANOVAResults method) (skbio.stats.gradient.GroupResults method) (skbio.stats.gradient.TrajectoryGradientANOVA method) (skbio.stats.gradient.WindowDifferenceGradientANOVA method) (skbio.stats.ordination.OrdinationResults method) (skbio.table.Table method) (skbio.tree.TreeNode method) (skbio.util.classproperty method) (skbio.workflow.method method) (skbio.workflow.requires method) (skbio.workflow.Workflow method) __get__() (skbio.util.classproperty method) __getitem__() (skbio.alignment.AlignmentStructure method) (skbio.alignment.TabularMSA method) (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) (skbio.table.Table method) (skbio.tree.TreeNode method) __getstate__() (skbio.alignment.AlignmentStructure method) (skbio.alignment.AlignPath method) (skbio.alignment.PairAlignPath method) (skbio.alignment.StripedSmithWaterman method) (skbio.alignment.TabularMSA method) (skbio.embedding.Embedding method) (skbio.embedding.ProteinEmbedding method) (skbio.embedding.ProteinVector method) (skbio.embedding.SequenceEmbedding method) (skbio.embedding.SequenceVector method) (skbio.io.registry.Format method) (skbio.io.registry.IORegistry method) (skbio.metadata.CategoricalMetadataColumn method) (skbio.metadata.Interval method) (skbio.metadata.IntervalMetadata method) (skbio.metadata.MetadataColumn method) (skbio.metadata.NumericMetadataColumn method) (skbio.metadata.SampleMetadata method) (skbio.sequence.DNA method) (skbio.sequence.GeneticCode method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) (skbio.stats.gradient.AverageGradientANOVA method) (skbio.stats.gradient.CategoryResults method) (skbio.stats.gradient.FirstDifferenceGradientANOVA method) (skbio.stats.gradient.GradientANOVA method) (skbio.stats.gradient.GradientANOVAResults method) (skbio.stats.gradient.GroupResults method) (skbio.stats.gradient.TrajectoryGradientANOVA method) (skbio.stats.gradient.WindowDifferenceGradientANOVA method) (skbio.stats.ordination.OrdinationResults method) (skbio.table.Table method) (skbio.tree.TreeNode method) (skbio.util.classproperty method) (skbio.workflow.method method) (skbio.workflow.requires method) (skbio.workflow.Workflow method) __gt__() (skbio.alignment.AlignmentStructure method) (skbio.alignment.AlignPath method) (skbio.alignment.PairAlignPath method) (skbio.alignment.StripedSmithWaterman method) (skbio.alignment.TabularMSA method) (skbio.embedding.Embedding method) (skbio.embedding.ProteinEmbedding method) (skbio.embedding.ProteinVector method) (skbio.embedding.SequenceEmbedding method) (skbio.embedding.SequenceVector method) (skbio.io.registry.Format method) (skbio.io.registry.IORegistry method) (skbio.metadata.CategoricalMetadataColumn method) (skbio.metadata.Interval method) (skbio.metadata.IntervalMetadata method) (skbio.metadata.MetadataColumn method) (skbio.metadata.NumericMetadataColumn method) (skbio.metadata.SampleMetadata method) (skbio.sequence.DNA method) (skbio.sequence.GeneticCode method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) (skbio.stats.gradient.AverageGradientANOVA method) (skbio.stats.gradient.CategoryResults method) (skbio.stats.gradient.FirstDifferenceGradientANOVA method) (skbio.stats.gradient.GradientANOVA method) (skbio.stats.gradient.GradientANOVAResults method) (skbio.stats.gradient.GroupResults method) (skbio.stats.gradient.TrajectoryGradientANOVA method) (skbio.stats.gradient.WindowDifferenceGradientANOVA method) (skbio.stats.ordination.OrdinationResults method) (skbio.table.Table method) (skbio.tree.TreeNode method) (skbio.util.classproperty method) (skbio.workflow.method method) (skbio.workflow.requires method) (skbio.workflow.Workflow method) __hash__() (skbio.alignment.AlignmentStructure method) (skbio.alignment.AlignPath method) (skbio.alignment.PairAlignPath method) (skbio.alignment.StripedSmithWaterman method) (skbio.embedding.Embedding method) (skbio.embedding.ProteinEmbedding method) (skbio.embedding.ProteinVector method) (skbio.embedding.SequenceEmbedding method) (skbio.embedding.SequenceVector method) (skbio.io.registry.Format method) (skbio.io.registry.IORegistry method) (skbio.stats.gradient.AverageGradientANOVA method) (skbio.stats.gradient.CategoryResults method) (skbio.stats.gradient.FirstDifferenceGradientANOVA method) (skbio.stats.gradient.GradientANOVA method) (skbio.stats.gradient.GradientANOVAResults method) (skbio.stats.gradient.GroupResults method) (skbio.stats.gradient.TrajectoryGradientANOVA method) (skbio.stats.gradient.WindowDifferenceGradientANOVA method) (skbio.stats.ordination.OrdinationResults method) (skbio.tree.TreeNode method) (skbio.util.classproperty method) (skbio.workflow.method method) (skbio.workflow.requires method) (skbio.workflow.Workflow method) __iter__() (skbio.alignment.TabularMSA method) (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.table.Table method) (skbio.tree.TreeNode method) __le__() (skbio.alignment.AlignmentStructure method) (skbio.alignment.AlignPath method) (skbio.alignment.PairAlignPath method) (skbio.alignment.StripedSmithWaterman method) (skbio.alignment.TabularMSA method) (skbio.embedding.Embedding method) (skbio.embedding.ProteinEmbedding method) (skbio.embedding.ProteinVector method) (skbio.embedding.SequenceEmbedding method) (skbio.embedding.SequenceVector method) (skbio.io.registry.Format method) (skbio.io.registry.IORegistry method) (skbio.metadata.CategoricalMetadataColumn method) (skbio.metadata.Interval method) (skbio.metadata.IntervalMetadata method) (skbio.metadata.MetadataColumn method) (skbio.metadata.NumericMetadataColumn method) (skbio.metadata.SampleMetadata method) (skbio.sequence.DNA method) (skbio.sequence.GeneticCode method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) (skbio.stats.gradient.AverageGradientANOVA method) (skbio.stats.gradient.CategoryResults method) (skbio.stats.gradient.FirstDifferenceGradientANOVA method) (skbio.stats.gradient.GradientANOVA method) (skbio.stats.gradient.GradientANOVAResults method) (skbio.stats.gradient.GroupResults method) (skbio.stats.gradient.TrajectoryGradientANOVA method) (skbio.stats.gradient.WindowDifferenceGradientANOVA method) (skbio.stats.ordination.OrdinationResults method) (skbio.table.Table method) (skbio.tree.TreeNode method) (skbio.util.classproperty method) (skbio.workflow.method method) (skbio.workflow.requires method) (skbio.workflow.Workflow method) __len__() (skbio.alignment.TabularMSA method) (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.tree.TreeNode method) __lt__() (skbio.alignment.AlignmentStructure method) (skbio.alignment.AlignPath method) (skbio.alignment.PairAlignPath method) (skbio.alignment.StripedSmithWaterman method) (skbio.alignment.TabularMSA method) (skbio.embedding.Embedding method) (skbio.embedding.ProteinEmbedding method) (skbio.embedding.ProteinVector method) (skbio.embedding.SequenceEmbedding method) (skbio.embedding.SequenceVector method) (skbio.io.registry.Format method) (skbio.io.registry.IORegistry method) (skbio.metadata.CategoricalMetadataColumn method) (skbio.metadata.Interval method) (skbio.metadata.IntervalMetadata method) (skbio.metadata.MetadataColumn method) (skbio.metadata.NumericMetadataColumn method) (skbio.metadata.SampleMetadata method) (skbio.sequence.DNA method) (skbio.sequence.GeneticCode method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) (skbio.stats.gradient.AverageGradientANOVA method) (skbio.stats.gradient.CategoryResults method) (skbio.stats.gradient.FirstDifferenceGradientANOVA method) (skbio.stats.gradient.GradientANOVA method) (skbio.stats.gradient.GradientANOVAResults method) (skbio.stats.gradient.GroupResults method) (skbio.stats.gradient.TrajectoryGradientANOVA method) (skbio.stats.gradient.WindowDifferenceGradientANOVA method) (skbio.stats.ordination.OrdinationResults method) (skbio.table.Table method) (skbio.tree.TreeNode method) (skbio.util.classproperty method) (skbio.workflow.method method) (skbio.workflow.requires method) (skbio.workflow.Workflow method) __ne__() (skbio.alignment.AlignmentStructure method) (skbio.alignment.AlignPath method) (skbio.alignment.PairAlignPath method) (skbio.alignment.StripedSmithWaterman method) (skbio.alignment.TabularMSA method) (skbio.embedding.Embedding method) (skbio.embedding.ProteinEmbedding method) (skbio.embedding.ProteinVector method) (skbio.embedding.SequenceEmbedding method) (skbio.embedding.SequenceVector method) (skbio.io.registry.Format method) (skbio.io.registry.IORegistry method) (skbio.metadata.CategoricalMetadataColumn method) (skbio.metadata.Interval method) (skbio.metadata.IntervalMetadata method) (skbio.metadata.MetadataColumn method) (skbio.metadata.NumericMetadataColumn method) (skbio.metadata.SampleMetadata method) (skbio.sequence.DNA method) (skbio.sequence.GeneticCode method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) (skbio.stats.gradient.AverageGradientANOVA method) (skbio.stats.gradient.CategoryResults method) (skbio.stats.gradient.FirstDifferenceGradientANOVA method) (skbio.stats.gradient.GradientANOVA method) (skbio.stats.gradient.GradientANOVAResults method) (skbio.stats.gradient.GroupResults method) (skbio.stats.gradient.TrajectoryGradientANOVA method) (skbio.stats.gradient.WindowDifferenceGradientANOVA method) (skbio.stats.ordination.OrdinationResults method) (skbio.table.Table method) (skbio.tree.TreeNode method) (skbio.util.classproperty method) (skbio.workflow.method method) (skbio.workflow.requires method) (skbio.workflow.Workflow method) __reversed__() (skbio.alignment.TabularMSA method) (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) __set__() (skbio.util.classproperty method) __set_name__() (skbio.util.classproperty method) __setstate__() (skbio.alignment.AlignmentStructure method) (skbio.alignment.StripedSmithWaterman method) __str__() (skbio.alignment.AlignmentStructure method) (skbio.alignment.AlignPath method) (skbio.alignment.PairAlignPath method) (skbio.alignment.StripedSmithWaterman method) (skbio.alignment.TabularMSA method) (skbio.embedding.Embedding method) (skbio.embedding.ProteinEmbedding method) (skbio.embedding.ProteinVector method) (skbio.embedding.SequenceEmbedding method) (skbio.embedding.SequenceVector method) (skbio.io.registry.Format method) (skbio.io.registry.IORegistry method) (skbio.metadata.CategoricalMetadataColumn method) (skbio.metadata.Interval method) (skbio.metadata.IntervalMetadata method) (skbio.metadata.MetadataColumn method) (skbio.metadata.NumericMetadataColumn method) (skbio.metadata.SampleMetadata method) (skbio.sequence.DNA method) (skbio.sequence.GeneticCode method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) (skbio.stats.gradient.AverageGradientANOVA method) (skbio.stats.gradient.CategoryResults method) (skbio.stats.gradient.FirstDifferenceGradientANOVA method) (skbio.stats.gradient.GradientANOVA method) (skbio.stats.gradient.GradientANOVAResults method) (skbio.stats.gradient.GroupResults method) (skbio.stats.gradient.TrajectoryGradientANOVA method) (skbio.stats.gradient.WindowDifferenceGradientANOVA method) (skbio.stats.ordination.OrdinationResults method) (skbio.table.Table method) (skbio.tree.TreeNode method) (skbio.util.classproperty method) (skbio.workflow.method method) (skbio.workflow.requires method) (skbio.workflow.Workflow method) A accumulate_to_ancestor() (skbio.tree.TreeNode method) ace() (in module skbio.diversity.alpha) add() (skbio.metadata.IntervalMetadata method) add_format() (skbio.io.registry.IORegistry method) add_group_metadata() (skbio.table.Table method) add_metadata() (skbio.table.Table method) align_to() (skbio.table.Table method) align_to_dataframe() (skbio.table.Table method) align_tree() (skbio.table.Table method) AlignmentStructure (class in skbio.alignment) AlignPath (class in skbio.alignment) alpha_diversity() (in module skbio.diversity) alr() (in module skbio.stats.composition) alr_inv() (in module skbio.stats.composition) ancestors() (skbio.tree.TreeNode method) ancom() (in module skbio.stats.composition) anosim() (in module skbio.stats.distance) append() (skbio.alignment.TabularMSA method) (skbio.tree.TreeNode method) ascii_art() (skbio.tree.TreeNode method) assert_data_frame_almost_equal() (in module skbio.util) assert_ordination_results_equal() (in module skbio.util) assign_ids() (skbio.tree.TreeNode method) assign_supports() (skbio.tree.TreeNode method) AverageGradientANOVA (class in skbio.stats.gradient) B berger_parker_d() (in module skbio.diversity.alpha) beta_diversity() (in module skbio.diversity) between() (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) bifurcate() (skbio.tree.TreeNode method) bioenv() (in module skbio.stats.distance) block_beta_diversity() (in module skbio.diversity) brillouin_d() (in module skbio.diversity.alpha) by_name() (skbio.sequence.SubstitutionMatrix class method) bytes() (skbio.embedding.Embedding method) (skbio.embedding.ProteinEmbedding method) (skbio.embedding.ProteinVector method) (skbio.embedding.SequenceEmbedding method) (skbio.embedding.SequenceVector method) C ca() (in module skbio.stats.ordination) cache_attr() (skbio.tree.TreeNode method) cardinal_to_ordinal() (in module skbio.util) CategoricalMetadataColumn (class in skbio.metadata) CategoryResults (class in skbio.stats.gradient) cca() (in module skbio.stats.ordination) centralize() (in module skbio.stats.composition) chao1() (in module skbio.diversity.alpha) chao1_ci() (in module skbio.diversity.alpha) classproperty (class in skbio.util) closure() (in module skbio.stats.composition) clr() (in module skbio.stats.composition) clr_inv() (in module skbio.stats.composition) collapse() (skbio.table.Table method) compare_rfd() (skbio.tree.TreeNode method) compare_subsets() (skbio.tree.TreeNode method) compare_tip_distances() (skbio.tree.TreeNode method) complement() (skbio.sequence.DNA method) (skbio.sequence.RNA method) concat() (skbio.metadata.IntervalMetadata class method) (skbio.sequence.DNA class method) (skbio.sequence.GrammaredSequence class method) (skbio.sequence.Protein class method) (skbio.sequence.RNA class method) (skbio.sequence.Sequence class method) (skbio.table.Table method) condensed_form() (skbio.stats.distance.DistanceMatrix method) confidence_bound() (in module skbio.stats.power) consensus() (skbio.alignment.TabularMSA method) conservation() (skbio.alignment.TabularMSA method) copy() (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) (skbio.table.Table method) (skbio.tree.TreeNode method) corr() (in module skbio.stats.ordination) count() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.tree.TreeNode method) create_caches() (skbio.tree.TreeNode method) create_format() (in module skbio.io.registry) (skbio.io.registry.IORegistry method) D data() (skbio.table.Table method) deepcopy() (skbio.tree.TreeNode method) definites() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) degap() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) degenerates() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) del_metadata() (skbio.table.Table method) deleter() (skbio.util.classproperty method) delimited_self() (skbio.table.Table method) descending_branch_length() (skbio.tree.TreeNode method) descriptive_equality() (skbio.table.Table method) dirmult_ttest() (in module skbio.stats.composition) DissimilarityMatrix (class in skbio.stats.distance) distance() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.tree.TreeNode method) DistanceMatrix (class in skbio.stats.distance) DNA (class in skbio.sequence) dominance() (in module skbio.diversity.alpha) doubles() (in module skbio.diversity.alpha) drop() (skbio.metadata.Interval method) (skbio.metadata.IntervalMetadata method) drop_missing_values() (skbio.metadata.CategoricalMetadataColumn method) (skbio.metadata.MetadataColumn method) (skbio.metadata.NumericMetadataColumn method) E e_matrix() (in module skbio.stats.ordination) EfficiencyWarning embed_vec_to_dataframe() (in module skbio.embedding) embed_vec_to_distances() (in module skbio.embedding) embed_vec_to_numpy() (in module skbio.embedding) embed_vec_to_ordination() (in module skbio.embedding) Embedding (class in skbio.embedding) enspie() (in module skbio.diversity.alpha) esty_ci() (in module skbio.diversity.alpha) example_table (in module skbio.table) exists() (skbio.table.Table method) expand_degenerates() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) extend() (skbio.alignment.TabularMSA method) (skbio.tree.TreeNode method) F f_matrix() (in module skbio.stats.ordination) faith_pd() (in module skbio.diversity.alpha) filter() (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) (skbio.table.Table method) filter_columns() (skbio.metadata.SampleMetadata method) filter_ids() (skbio.metadata.CategoricalMetadataColumn method) (skbio.metadata.MetadataColumn method) (skbio.metadata.NumericMetadataColumn method) (skbio.metadata.SampleMetadata method) find() (skbio.tree.TreeNode method) find_all() (skbio.tree.TreeNode method) find_by_func() (skbio.tree.TreeNode method) find_by_id() (skbio.tree.TreeNode method) find_duplicates() (in module skbio.util) find_motifs() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) find_with_regex() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) FirstDifferenceGradientANOVA (class in skbio.stats.gradient) fisher_alpha() (in module skbio.diversity.alpha) Format (class in skbio.io.registry) frequencies() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) from_adjacency() (skbio.table.Table static method) from_bits() (skbio.alignment.AlignPath class method) (skbio.alignment.PairAlignPath class method) from_cigar() (skbio.alignment.PairAlignPath class method) from_coordinates() (skbio.alignment.AlignPath class method) (skbio.alignment.PairAlignPath class method) from_dict() (skbio.alignment.TabularMSA class method) (skbio.sequence.SubstitutionMatrix class method) from_hdf5() (skbio.table.Table class method) from_indices() (skbio.alignment.AlignPath class method) (skbio.alignment.PairAlignPath class method) from_iterable() (skbio.sequence.SubstitutionMatrix class method) (skbio.stats.distance.DissimilarityMatrix class method) (skbio.stats.distance.DistanceMatrix class method) from_json() (skbio.table.Table class method) from_linkage_matrix() (skbio.tree.TreeNode class method) from_ncbi() (skbio.sequence.GeneticCode class method) from_path_seqs() (skbio.alignment.TabularMSA class method) from_tabular() (skbio.alignment.AlignPath class method) (skbio.alignment.PairAlignPath class method) from_taxdump() (skbio.tree.TreeNode class method) from_taxonomy() (skbio.tree.TreeNode class method) from_tsv() (skbio.table.Table static method) G gap_frequencies() (skbio.alignment.TabularMSA method) gaps() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) gc_content() (skbio.sequence.DNA method) (skbio.sequence.RNA method) gc_frequency() (skbio.sequence.DNA method) (skbio.sequence.RNA method) GeneticCode (class in skbio.sequence) get_alpha_diversity_metrics() (in module skbio.diversity) get_beta_diversity_metrics() (in module skbio.diversity) get_column() (skbio.metadata.SampleMetadata method) get_data_path() (in module skbio.util) get_ids() (skbio.metadata.CategoricalMetadataColumn method) (skbio.metadata.MetadataColumn method) (skbio.metadata.NumericMetadataColumn method) (skbio.metadata.SampleMetadata method) get_max_distance() (skbio.tree.TreeNode method) get_missing() (skbio.metadata.CategoricalMetadataColumn method) (skbio.metadata.MetadataColumn method) (skbio.metadata.NumericMetadataColumn method) get_names() (skbio.sequence.SubstitutionMatrix class method) get_reader() (skbio.io.registry.IORegistry method) get_sniffer() (skbio.io.registry.IORegistry method) get_table_density() (skbio.table.Table method) get_trajectories() (skbio.stats.gradient.AverageGradientANOVA method) (skbio.stats.gradient.FirstDifferenceGradientANOVA method) (skbio.stats.gradient.GradientANOVA method) (skbio.stats.gradient.TrajectoryGradientANOVA method) (skbio.stats.gradient.WindowDifferenceGradientANOVA method) get_value() (skbio.metadata.CategoricalMetadataColumn method) (skbio.metadata.MetadataColumn method) (skbio.metadata.NumericMetadataColumn method) get_value_by_ids() (skbio.table.Table method) get_writer() (skbio.io.registry.IORegistry method) getter() (skbio.util.classproperty method) gini_index() (in module skbio.diversity.alpha) global_pairwise_align() (in module skbio.alignment) global_pairwise_align_nucleotide() (in module skbio.alignment) global_pairwise_align_protein() (in module skbio.alignment) goods_coverage() (in module skbio.diversity.alpha) GradientANOVA (class in skbio.stats.gradient) GradientANOVAResults (class in skbio.stats.gradient) GrammaredSequence (class in skbio.sequence) group_metadata() (skbio.table.Table method) GroupResults (class in skbio.stats.gradient) H hamming() (in module skbio.sequence.distance) has_children() (skbio.tree.TreeNode method) has_definites() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) has_degenerates() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) has_gaps() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) has_interval_metadata() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) has_metadata() (skbio.alignment.TabularMSA method) (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) has_missing_values() (skbio.metadata.CategoricalMetadataColumn method) (skbio.metadata.MetadataColumn method) (skbio.metadata.NumericMetadataColumn method) has_nondegenerates() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) has_positional_metadata() (skbio.alignment.TabularMSA method) (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) has_stops() (skbio.sequence.Protein method) head() (skbio.table.Table method) heip_e() (in module skbio.diversity.alpha) hill() (in module skbio.diversity.alpha) hommola_cospeciation() (in module skbio.stats.evolve) I identity() (skbio.sequence.SubstitutionMatrix class method) ids() (skbio.table.Table method) ilr() (in module skbio.stats.composition) ilr_inv() (in module skbio.stats.composition) index() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) (skbio.table.Table method) index_tree() (skbio.tree.TreeNode method) initialize_state() (skbio.workflow.Workflow method) inner() (in module skbio.stats.composition) insert() (skbio.tree.TreeNode method) Interval (class in skbio.metadata) IntervalMetadata (class in skbio.metadata) inv_simpson() (in module skbio.diversity.alpha) invalidate_caches() (skbio.tree.TreeNode method) IORegistry (class in skbio.io.registry) is_empty() (skbio.table.Table method) is_reverse_complement() (skbio.sequence.DNA method) (skbio.sequence.RNA method) is_root() (skbio.tree.TreeNode method) is_tip() (skbio.tree.TreeNode method) is_zero_based() (skbio.alignment.AlignmentStructure method) isubsample() (in module skbio.stats) iter() (skbio.table.Table method) iter_contiguous() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) iter_data() (skbio.table.Table method) iter_kmers() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) iter_pairwise() (skbio.table.Table method) iter_positions() (skbio.alignment.TabularMSA method) J join() (skbio.alignment.TabularMSA method) K kempton_taylor_q() (in module skbio.diversity.alpha) kmer_distance() (in module skbio.sequence.distance) kmer_frequencies() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) L lca() (skbio.tree.TreeNode method) length() (skbio.table.Table method) levelorder() (skbio.tree.TreeNode method) list_read_formats() (skbio.io.registry.IORegistry method) list_write_formats() (skbio.io.registry.IORegistry method) lladser_ci() (in module skbio.diversity.alpha) lladser_pe() (in module skbio.diversity.alpha) load() (skbio.metadata.SampleMetadata class method) local_pairwise_align() (in module skbio.alignment) local_pairwise_align_nucleotide() (in module skbio.alignment) local_pairwise_align_protein() (in module skbio.alignment) local_pairwise_align_ssw() (in module skbio.alignment) lowercase() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) lowest_common_ancestor() (skbio.tree.TreeNode method) M majority_rule() (in module skbio.tree) make_identity_substitution_matrix() (in module skbio.alignment) mantel() (in module skbio.stats.distance) margalef() (in module skbio.diversity.alpha) match_frequency() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) matches() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) max() (skbio.table.Table method) mcintosh_d() (in module skbio.diversity.alpha) mcintosh_e() (in module skbio.diversity.alpha) mean_and_std() (in module skbio.stats.ordination) menhinick() (in module skbio.diversity.alpha) merge() (skbio.metadata.IntervalMetadata method) (skbio.metadata.SampleMetadata method) (skbio.table.Table method) metadata() (skbio.table.Table method) metadata_to_dataframe() (skbio.table.Table method) MetadataColumn (class in skbio.metadata) method (class in skbio.workflow) michaelis_menten_fit() (in module skbio.diversity.alpha) min() (skbio.table.Table method) mismatch_frequency() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) mismatches() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) module skbio.alignment skbio.diversity skbio.diversity.alpha skbio.diversity.beta skbio.embedding skbio.io skbio.io.format.binary_dm skbio.io.format.biom skbio.io.format.blast6 skbio.io.format.blast7 skbio.io.format.clustal skbio.io.format.embed skbio.io.format.embl skbio.io.format.fasta skbio.io.format.fastq skbio.io.format.genbank skbio.io.format.gff3 skbio.io.format.lsmat skbio.io.format.newick skbio.io.format.ordination skbio.io.format.phylip skbio.io.format.qseq skbio.io.format.sample_metadata skbio.io.format.stockholm skbio.io.format.taxdump skbio.io.registry skbio.io.util skbio.metadata skbio.sequence skbio.sequence.distance skbio.stats skbio.stats.composition skbio.stats.distance skbio.stats.evolve skbio.stats.gradient skbio.stats.ordination skbio.stats.power skbio.table skbio.tree skbio.util skbio.workflow monkey_patch() (skbio.io.registry.IORegistry method) multi_replace() (in module skbio.stats.composition) multiplicative_replacement() (in module skbio.stats.composition) N neighbors() (skbio.tree.TreeNode method) nj() (in module skbio.tree) nni() (in module skbio.tree) non_tips() (skbio.tree.TreeNode method) nondegenerates() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) nonzero() (skbio.table.Table method) nonzero_counts() (skbio.table.Table method) norm() (skbio.table.Table method) NumericMetadataColumn (class in skbio.metadata) O observed_features() (in module skbio.diversity.alpha) observed_node_counts() (skbio.tree.TreeNode method) observed_otus() (in module skbio.diversity.alpha) open() (in module skbio.io.util) open_file() (in module skbio.io.util) open_files() (in module skbio.io.util) OrdinationResults (class in skbio.stats.ordination) osd() (in module skbio.diversity.alpha) P pa() (skbio.table.Table method) PairAlignPath (class in skbio.alignment) paired_subsamples() (in module skbio.stats.power) pairwise_vlr() (in module skbio.stats.composition) partial_beta_diversity() (in module skbio.diversity) partition() (skbio.table.Table method) pcoa() (in module skbio.stats.ordination) pcoa_biplot() (in module skbio.stats.ordination) permanova() (in module skbio.stats.distance) permdisp() (in module skbio.stats.distance) permute() (skbio.stats.distance.DistanceMatrix method) perturb() (in module skbio.stats.composition) perturb_inv() (in module skbio.stats.composition) phydiv() (in module skbio.diversity.alpha) pielou_e() (in module skbio.diversity.alpha) plot() (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) (skbio.stats.ordination.OrdinationResults method) pop() (skbio.tree.TreeNode method) postorder() (skbio.tree.TreeNode method) power() (in module skbio.stats.composition) pre_and_postorder() (skbio.tree.TreeNode method) preorder() (skbio.tree.TreeNode method) Protein (class in skbio.sequence) ProteinEmbedding (class in skbio.embedding) ProteinVector (class in skbio.embedding) prune() (skbio.tree.TreeNode method) pwmantel() (in module skbio.stats.distance) Q query() (skbio.metadata.IntervalMetadata method) R randdm() (in module skbio.stats.distance) rankdata() (skbio.table.Table method) rda() (in module skbio.stats.ordination) read() (in module skbio.io.registry) (skbio.alignment.TabularMSA class method) (skbio.embedding.ProteinEmbedding class method) (skbio.embedding.ProteinVector class method) (skbio.io.registry.IORegistry method) (skbio.metadata.IntervalMetadata class method) (skbio.metadata.SampleMetadata class method) (skbio.sequence.DNA class method) (skbio.sequence.GrammaredSequence class method) (skbio.sequence.Protein class method) (skbio.sequence.RNA class method) (skbio.sequence.Sequence class method) (skbio.sequence.SubstitutionMatrix class method) (skbio.stats.distance.DissimilarityMatrix class method) (skbio.stats.distance.DistanceMatrix class method) (skbio.stats.ordination.OrdinationResults class method) (skbio.table.Table class method) (skbio.tree.TreeNode class method) reader() (skbio.io.registry.Format method) reassign_index() (skbio.alignment.TabularMSA method) reduce() (skbio.table.Table method) redundant_form() (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) remove() (skbio.tree.TreeNode method) remove_deleted() (skbio.tree.TreeNode method) remove_empty() (skbio.table.Table method) rename() (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) (skbio.stats.ordination.OrdinationResults method) renyi() (in module skbio.diversity.alpha) replace() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) RepresentationWarning requires (class in skbio.workflow) reverse_complement() (skbio.sequence.DNA method) (skbio.sequence.RNA method) reverse_transcribe() (skbio.sequence.RNA method) RNA (class in skbio.sequence) robbins() (in module skbio.diversity.alpha) root() (skbio.tree.TreeNode method) root_at() (skbio.tree.TreeNode method) root_at_midpoint() (skbio.tree.TreeNode method) root_by_outgroup() (skbio.tree.TreeNode method) S safe_md5() (in module skbio.util) SampleMetadata (class in skbio.metadata) save() (skbio.metadata.CategoricalMetadataColumn method) (skbio.metadata.MetadataColumn method) (skbio.metadata.NumericMetadataColumn method) (skbio.metadata.SampleMetadata method) sbp_basis() (in module skbio.stats.composition) scale() (in module skbio.stats.ordination) Sequence (class in skbio.sequence) SequenceEmbedding (class in skbio.embedding) SequenceVector (class in skbio.embedding) set_zero_based() (skbio.alignment.AlignmentStructure method) setter() (skbio.util.classproperty method) shannon() (in module skbio.diversity.alpha) shear() (skbio.tree.TreeNode method) shuffle() (skbio.tree.TreeNode method) siblings() (skbio.tree.TreeNode method) simpson() (in module skbio.diversity.alpha) simpson_d() (in module skbio.diversity.alpha) simpson_e() (in module skbio.diversity.alpha) singles() (in module skbio.diversity.alpha) skbio.alignment module skbio.diversity module skbio.diversity.alpha module skbio.diversity.beta module skbio.embedding module skbio.io module skbio.io.format.binary_dm module skbio.io.format.biom module skbio.io.format.blast6 module skbio.io.format.blast7 module skbio.io.format.clustal module skbio.io.format.embed module skbio.io.format.embl module skbio.io.format.fasta module skbio.io.format.fastq module skbio.io.format.genbank module skbio.io.format.gff3 module skbio.io.format.lsmat module skbio.io.format.newick module skbio.io.format.ordination module skbio.io.format.phylip module skbio.io.format.qseq module skbio.io.format.sample_metadata module skbio.io.format.stockholm module skbio.io.format.taxdump module skbio.io.registry module skbio.io.util module skbio.metadata module skbio.sequence module skbio.sequence.distance module skbio.stats module skbio.stats.composition module skbio.stats.distance module skbio.stats.evolve module skbio.stats.gradient module skbio.stats.ordination module skbio.stats.power module skbio.table module skbio.tree module skbio.util module skbio.workflow module sniff() (in module skbio.io.registry) (skbio.io.registry.IORegistry method) sniffer() (skbio.io.registry.Format method) sobs() (in module skbio.diversity.alpha) sort() (skbio.alignment.TabularMSA method) (skbio.metadata.IntervalMetadata method) (skbio.table.Table method) sort_order() (skbio.table.Table method) stops() (skbio.sequence.Protein method) StripedSmithWaterman (class in skbio.alignment) strong() (in module skbio.diversity.alpha) subsample() (skbio.table.Table method) subsample_counts() (in module skbio.stats) subsample_paired_power() (in module skbio.stats.power) subsample_power() (in module skbio.stats.power) subset() (skbio.tree.TreeNode method) subsets() (skbio.tree.TreeNode method) SubstitutionMatrix (class in skbio.sequence) subtree() (skbio.tree.TreeNode method) sum() (skbio.table.Table method) svd_rank() (in module skbio.stats.ordination) T Table (class in skbio.table) TabularMSA (class in skbio.alignment) tip_tip_distances() (skbio.tree.TreeNode method) tips() (skbio.tree.TreeNode method) to_anndata() (skbio.table.Table method) to_array() (skbio.tree.TreeNode method) to_bits() (skbio.alignment.AlignPath method) (skbio.alignment.PairAlignPath method) to_cigar() (skbio.alignment.PairAlignPath method) to_coordinates() (skbio.alignment.AlignPath method) (skbio.alignment.PairAlignPath method) to_data_frame() (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) to_dataframe() (skbio.metadata.CategoricalMetadataColumn method) (skbio.metadata.MetadataColumn method) (skbio.metadata.NumericMetadataColumn method) (skbio.metadata.SampleMetadata method) (skbio.table.Table method) to_definites() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) to_dict() (skbio.alignment.TabularMSA method) (skbio.sequence.SubstitutionMatrix method) to_files() (skbio.stats.gradient.CategoryResults method) (skbio.stats.gradient.GradientANOVAResults method) (skbio.stats.gradient.GroupResults method) to_hdf5() (skbio.table.Table method) to_indices() (skbio.alignment.AlignPath method) (skbio.alignment.PairAlignPath method) (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) to_json() (skbio.table.Table method) to_regex() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) to_series() (skbio.metadata.CategoricalMetadataColumn method) (skbio.metadata.MetadataColumn method) (skbio.metadata.NumericMetadataColumn method) (skbio.stats.distance.DistanceMatrix method) to_taxonomy() (skbio.tree.TreeNode method) to_tsv() (skbio.table.Table method) TrajectoryGradientANOVA (class in skbio.stats.gradient) transcribe() (skbio.sequence.DNA method) transform() (skbio.table.Table method) translate() (skbio.sequence.DNA method) (skbio.sequence.GeneticCode method) (skbio.sequence.RNA method) translate_six_frames() (skbio.sequence.DNA method) (skbio.sequence.GeneticCode method) (skbio.sequence.RNA method) transpose() (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) (skbio.table.Table method) traverse() (skbio.tree.TreeNode method) tree_basis() (in module skbio.stats.composition) TreeNode (class in skbio.tree) tsallis() (in module skbio.diversity.alpha) U unpack() (skbio.tree.TreeNode method) unpack_by_func() (skbio.tree.TreeNode method) unroot() (skbio.tree.TreeNode method) unrooted_copy() (skbio.tree.TreeNode method) unrooted_deepcopy() (skbio.tree.TreeNode method) unrooted_move() (skbio.tree.TreeNode method) unweighted_unifrac() (in module skbio.diversity.beta) update_ids() (skbio.table.Table method) V vlr() (in module skbio.stats.composition) W weighted_unifrac() (in module skbio.diversity.beta) WindowDifferenceGradientANOVA (class in skbio.stats.gradient) within() (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) Workflow (class in skbio.workflow) write() (in module skbio.io.registry) (skbio.alignment.TabularMSA method) (skbio.embedding.ProteinEmbedding method) (skbio.embedding.ProteinVector method) (skbio.io.registry.IORegistry method) (skbio.metadata.IntervalMetadata method) (skbio.metadata.SampleMetadata method) (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.sequence.SubstitutionMatrix method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.distance.DistanceMatrix method) (skbio.stats.ordination.OrdinationResults method) (skbio.table.Table method) (skbio.tree.TreeNode method) writer() (skbio.io.registry.Format method)
