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is QIIME 2?","Community","Core concepts","Data resources","Getting started","Glossary","QIIME 2 user documentation","Installing QIIME 2","Natively installing QIIME 2","Installing QIIME 2 using Amazon Web Services","Installing QIIME 2 using Docker","Installing QIIME 2 using Virtual Machines","Installing QIIME 2 using VirtualBox","Artifact API","Interfaces","QIIME 2 command-line interface (q2cli)","QIIME 2 Studio (q2studio)","alignment","mafft: De novo multiple sequence alignment with MAFFT","mask: Positional conservation and gap filtering.","add_pseudocount: Add pseudocount to table","ancom: Apply ANCOM to identify features that differ in abundance.","composition","denoise_paired: Denoise and dereplicate paired-end sequences","denoise_single: Denoise and dereplicate single-end sequences","dada2","plot_qualities: Plot positional qualitites","emp_paired: Demultiplex paired-end sequence data generated with the EMP protocol.","emp_single: Demultiplex sequence data generated with the EMP protocol.","demux","summarize: Summarize counts per sample.","alpha: Alpha diversity","alpha_correlation: Alpha diversity correlation","alpha_group_significance: Alpha diversity comparisons","alpha_phylogenetic: Alpha diversity (phylogenetic)","beta: Beta diversity","beta_group_significance: Beta diversity group significance","beta_phylogenetic: Beta diversity (phylogenetic)","bioenv: bioenv","core_metrics: Core diversity metrics","filter_distance_matrix: Filter samples from a distance matrix.","diversity","pcoa: Principal Coordinate Analysis","emperor","plot: Visualize and Interact with Principal Coordinates Analysis Plots","classify: Classify reads by taxon.","extract_reads: Extract reads from reference.","fit_classifier: Train a scikit-learn classifier.","fit_classifier_naive_bayes: Train the naive_bayes classifier.","feature-classifier","filter_features: Filter features from table.","filter_samples: Filter samples from table.","feature-table","merge: Combine two 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