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..
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add_alpha_to_mapping_file
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add_qiime_labels
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adjust_seq_orientation
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align_seqs
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alpha_diversity
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alpha_rarefaction
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ampliconnoise
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assign_taxonomy
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beta_diversity
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beta_diversity_through_plots
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beta_significance
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blast_wrapper
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cluster_quality
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collapse_samples
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collate_alpha
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compare_alpha_diversity
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compare_categories
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compare_distance_matrices
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compare_taxa_summaries
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compare_trajectories
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compute_core_microbiome
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compute_taxonomy_ratios
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conditional_uncovered_probability
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consensus_tree
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convert_fastaqual_fastq
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core_diversity_analyses
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count_seqs
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demultiplex_fasta
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denoiser_preprocess
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differential_abundance
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dissimilarity_mtx_stats
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distance_matrix_from_mapping
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estimate_observation_richness
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exclude_seqs_by_blast
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extract_reads_from_interleaved_file
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extract_seqs_by_sample_id
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filter_alignment
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filter_distance_matrix
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filter_fasta
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filter_otus_by_sample
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filter_otus_from_otu_table
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filter_samples_from_otu_table
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filter_taxa_from_otu_table
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filter_tree
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fix_arb_fasta
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group_significance
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identify_chimeric_seqs
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identify_missing_files
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identify_paired_differences
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inflate_denoiser_output
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jackknifed_beta_diversity
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join_paired_ends
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make_2d_plots
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make_bipartite_network
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make_bootstrapped_tree
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make_distance_boxplots
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make_distance_comparison_plots
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make_fastq
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make_otu_heatmap
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make_otu_network
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make_otu_table
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make_phylogeny
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make_prefs_file
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make_rarefaction_plots
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make_tep
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map_reads_to_reference
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merge_mapping_files
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merge_otu_maps
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merge_otu_tables
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multiple_extract_barcodes
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multiple_join_paired_ends
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multiple_rarefactions
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multiple_rarefactions_even_depth
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multiple_split_libraries_fastq
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neighbor_joining
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nmds
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normalize_table
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observation_metadata_correlation
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parallel_align_seqs_pynast
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parallel_alpha_diversity
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parallel_assign_taxonomy_blast
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parallel_assign_taxonomy_rdp
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parallel_assign_taxonomy_uclust
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parallel_beta_diversity
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parallel_blast
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parallel_identify_chimeric_seqs
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parallel_map_reads_to_reference
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parallel_merge_otu_tables
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parallel_multiple_rarefactions
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parallel_pick_otus_blast
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parallel_pick_otus_sortmerna
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parallel_pick_otus_trie
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parallel_pick_otus_uclust_ref
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parallel_pick_otus_usearch61_ref
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pick_closed_reference_otus
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pick_de_novo_otus
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pick_open_reference_otus
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pick_otus
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pick_rep_set
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plot_rank_abundance_graph
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plot_semivariogram
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plot_taxa_summary
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poller
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principal_coordinates
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print_metadata_stats
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quality_scores_plot
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relatedness
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shared_phylotypes
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simsam
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single_rarefaction
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sort_otu_table
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split_libraries
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split_libraries_fastq
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split_libraries_lea_seq
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split_otu_table
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split_otu_table_by_taxonomy
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split_sequence_file_on_sample_ids
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start_parallel_jobs
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start_parallel_jobs_sc
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start_parallel_jobs_torque
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subsample_fasta
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summarize_taxa
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summarize_taxa_through_plots
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supervised_learning
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transform_coordinate_matrices
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tree_compare
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trflp_file_to_otu_table
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truncate_fasta_qual_files
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truncate_reverse_primer
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unweight_fasta
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upgma_cluster
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validate_mapping_file
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__init__.py
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