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