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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","denoise_16S: Deblur sequences using a 16S positive filter.","denoise_other: Deblur sequences using a user-specified positive filter.","deblur","visualize_stats: Visualize Deblur stats per sample.","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_correlation: Beta diversity correlation","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_consensus_blast: BLAST+ consensus taxonomy classifier","classify_consensus_vsearch: VSEARCH 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phylogenetic tree.","quality-filter","q_score: Quality filter based on sequence quality scores.","visualize_stats: Visualize filtering stats per sample.","barplot: Visualize taxonomy with an interactive bar plot","collapse: Collapse features by their taxonomy at the specified level","taxa","tabulate: View taxonomy associated with each feature","types","Developing a QIIME 2 plugin","Future plugins","Plugins","Semantic types","Supplementary resources","&#8220;Atacama soil microbiome&#8221; tutorial","Exporting data","Training feature classifiers with q2-feature-classifier","Filtering data","Fecal microbiota transplant (FMT) study: an exercise","Importing data","Tutorials","&#8220;Moving Pictures&#8221; tutorial","Upgrading QIIME 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