Index

A

add_alpha_to_mapping_file.py add_qiime_labels.py adjust_seq_orientation.py align_seqs.py alpha_diversity.py

alpha_diversity_metrics alpha_rarefaction.py ampliconnoise.py assign_taxonomy.py

B

beta_diversity.py beta_diversity_metrics beta_diversity_through_plots.py

beta_significance.py blast_wrapper.py

C

categorized_dist_scatterplot.py check_id_map.py clean_raxml_parsimony_tree.py cluster_quality.py collate_alpha.py compare_3d_plots.py compare_alpha_diversity.py compare_categories.py compare_distance_matrices.py compare_taxa_summaries.py compute_core_microbiome.py

conditional_uncovered_probability.py consensus_tree.py convert_fastaqual_fastq.py convert_fastaqual_to_fastq.py convert_otu_table_to_unifrac_sample_mapping.py convert_unifrac_sample_mapping_to_otu_table.py core_diversity_analyses.py core_qiime_analyses.py count_seqs.py cytoscape, [1]

D

demultiplex_fasta.py denoise_wrapper.py denoiser.py denoiser_preprocess.py denoiser_worker.py

detrend.py dissimilarity_mtx_stats.py distance_matrix_from_mapping.py Documentation

E

exclude_seqs_by_blast.py

extract_seqs_by_sample_id.py

F

filter_alignment.py filter_distance_matrix.py filter_fasta.py filter_otus_by_sample.py filter_otus_from_otu_table.py

filter_samples_from_otu_table.py filter_taxa_from_otu_table.py filter_tree.py fix_arb_fasta.py

I

identify_chimeric_seqs.py identify_missing_files.py inflate_denoiser_output.py

insert_seqs_into_tree.py Installing QIIME

J

jackknifed_beta_diversity.py

L

load_remote_mapping_file.py

M

make_2d_plots.py make_3d_plots.py make_bipartite_network.py make_bootstrapped_tree.py make_distance_boxplots.py make_distance_comparison_plots.py make_distance_histograms.py make_fastq.py make_library_id_lists.py make_otu_heatmap.py make_otu_heatmap_html.py make_otu_network.py make_otu_table.py

make_per_library_sff.py make_phylogeny.py make_prefs_file.py make_qiime_py_file.py make_qiime_rst_file.py make_rarefaction_plots.py make_tep.py map_reads_to_reference.py merge_mapping_files.py merge_otu_maps.py merge_otu_tables.py multiple_rarefactions.py multiple_rarefactions_even_depth.py

N

neighbor_joining.py

nmds.py

O

otu_category_significance.py

P

parallel_align_seqs_pynast.py parallel_alpha_diversity.py parallel_assign_taxonomy_blast.py parallel_assign_taxonomy_rdp.py parallel_beta_diversity.py parallel_blast.py parallel_identify_chimeric_seqs.py parallel_map_reads_to_reference.py parallel_multiple_rarefactions.py parallel_pick_otus_blast.py parallel_pick_otus_trie.py parallel_pick_otus_uclust_ref.py parallel_pick_otus_usearch61_ref.py pick_closed_reference_otus.py pick_de_novo_otus.py pick_open_reference_otus.py pick_otus.py

pick_otus_through_otu_table.py pick_reference_otus_through_otu_table.py pick_rep_set.py pick_subsampled_reference_otus_through_otu_table.py plot_rank_abundance_graph.py plot_semivariogram.py plot_taxa_summary.py poller.py poller_example.py pool_by_metadata.py preferences_file principal_coordinates.py print_metadata_stats.py print_qiime_config.py process_iseq.py process_qseq.py process_sff.py

Q

quality_scores_plot.py

R

relatedness.py

S

shared_phylotypes.py simsam.py single_rarefaction.py sort_otu_table.py split_fasta_on_sample_ids.py split_libraries.py split_libraries_fastq.py split_otu_table.py split_otu_table_by_taxonomy.py

start_parallel_jobs.py start_parallel_jobs_sc.py start_parallel_jobs_torque.py submit_to_mgrast.py subsample_fasta.py summarize_otu_by_cat.py summarize_taxa.py summarize_taxa_through_plots.py supervised_learning.py

T

transform_coordinate_matrices.py tree_compare.py trflp_file_to_otu_table.py

trim_sff_primers.py truncate_fasta_qual_files.py truncate_reverse_primer.py

U

unweight_fasta.py

upgma_cluster.py

V

validate_demultiplexed_fasta.py