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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","demux-paired: Demultiplex paired-end sequence data with barcodes in-sequence.","demux-single: Demultiplex single-end sequence data with barcodes in-sequence.","cutadapt","trim-paired: Find and remove adapters in demultiplexed paired-end sequences.","trim-single: Find and remove adapters in demultiplexed single-end sequences.","denoise-paired: Denoise and dereplicate paired-end sequences","denoise-pyro: Denoise and dereplicate single-end pyrosequences","denoise-single: Denoise and dereplicate single-end sequences","dada2","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)","alpha-rarefaction: Alpha rarefaction curves","beta: Beta diversity","beta-group-significance: Beta diversity group significance","beta-phylogenetic: Beta diversity (phylogenetic)","beta-phylogenetic-alt: Beta diversity (phylogenetic) - High Performance Computation","beta-rarefaction: Beta diversity rarefaction","bioenv: bioenv","core-metrics: Core diversity metrics (non-phylogenetic)","core-metrics-phylogenetic: Core diversity metrics (phylogenetic and non-phylogenetic)","filter-distance-matrix: Filter samples from a distance matrix.","diversity","mantel: Apply the Mantel test to two distance matrices","pcoa: Principal Coordinate Analysis","procrustes-analysis: Procrustes Analysis","emperor","plot: Visualize and Interact with Principal Coordinates Analysis Plots","procrustes-plot: Visualize and Interact with a procrustes plot","classify-consensus-blast: BLAST+ consensus taxonomy classifier","classify-consensus-vsearch: VSEARCH consensus taxonomy classifier","classify-sklearn: Pre-fitted sklearn-based taxonomy classifier","extract-reads: Extract reads from reference","fit-classifier-naive-bayes: Train the naive_bayes 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Balance Summary","correlation-clustering: Hierarchical clustering using feature correlation.","dendrogram-heatmap: Dendrogram heatmap.","gradient-clustering: Hierarchical clustering using gradient information.","ilr-transform: Isometric Log-ratio Transform","gneiss","lme-regression: Simplicial Linear mixed effects regression","ols-regression: Simplicial Ordinary Least Squares Regression","Available plugins","first-differences: Compute first differences or difference from baseline between sequential states","first-distances: Compute first distances or distance from baseline between sequential states","longitudinal","linear-mixed-effects: Linear mixed effects modeling","nmit: Nonparametric microbial interdependence test","pairwise-differences: Paired difference testing and boxplots","pairwise-distances: Paired pairwise distance testing and boxplots","volatility: Volatility analysis","distance-matrix: Create a distance matrix from a numeric Metadata column","metadata","tabulate: Interactively explore Metadata in an HTML table","fasttree: Construct a phylogenetic tree with FastTree.","filter-table: Remove features from table if they&#8217;re not present in tree.","phylogeny","midpoint-root: Midpoint root an unrooted phylogenetic tree.","evaluate-composition: Evaluate expected vs. observed taxonomic composition of samples","evaluate-seqs: Compare query (observed) vs. reference (expected) sequences.","exclude-seqs: Exclude sequences by alignment","quality-control","quality-filter","q-score: Quality filter based on sequence quality scores.","q-score-joined: Quality filter based on joined sequence quality scores.","classify-samples: Supervised learning classifier.","sample-classifier","maturity-index: Microbial maturity index prediction.","regress-samples: Supervised learning regressor.","barplot: Visualize taxonomy with an interactive bar plot","collapse: Collapse features by their taxonomy at the specified level","filter-seqs: Taxonomy-based feature sequence 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