├── .mailmap ├── CONTRIBUTING.md ├── COPYING.txt ├── ChangeLog.md ├── MANIFEST.in ├── README.md ├── doc ├── Makefile ├── README ├── _static │ ├── Examples │ │ └── File_Formats │ │ │ ├── Example_ID_to_Taxonomy_mapping_File.txt │ │ │ ├── Example_Mapping_File.txt │ │ │ ├── Fasting_Map_reverse_primers.txt │ │ │ └── example_fasta_after_split_libraries.fna │ ├── PoweredByPycogent.jpg │ ├── basic.css │ ├── default.css │ ├── favicon.ico │ ├── google_feed.js │ ├── powered_by_skbio.png │ ├── qiime_logo_large.png │ └── wordpressheader.png ├── _templates │ └── layout.html ├── conf.py ├── developer │ ├── index.rst │ └── script_testing.rst ├── documentation │ ├── biom_format.rst │ ├── file_formats.rst │ ├── index.rst │ ├── qiime_parameters_files.rst │ ├── script_index.rst │ └── table_objects.rst ├── images │ ├── UPGMAbytreatment.png │ ├── barchart1.png │ ├── biplot.png │ ├── boottree.png │ ├── configure_ebs_volume_attachment.png │ ├── configure_ebs_volume_creation.png │ ├── create_an_ebs_volume.png │ ├── cyberduck_create_output_file.png │ ├── cyberduck_drag_and_drop_input_file.png │ ├── cyberduck_drag_and_drop_output_file.png │ ├── cyberduck_open_connection.png │ ├── cyberduck_opened_connection.png │ ├── cyberduck_view_file.png │ ├── cytoscape_change_background.png │ ├── cytoscape_colored_edges.png │ ├── cytoscape_colored_shared.png │ ├── cytoscape_initial_network.png │ ├── cytoscape_nodecolor.png │ ├── distance_boxplots1.png │ ├── example_primer_construct.png │ ├── favicon.ico │ ├── fisheyeheatmap.png │ ├── header.png │ ├── heatmap.png │ ├── hiarchclust.png │ ├── jackpcoa.png │ ├── mantel_correlogram.png │ ├── network.png │ ├── pcoa1.png │ ├── procrustes_tutorial_figure1.png │ ├── public_dns_entry.png │ ├── qiime_logo_large.png │ ├── rarecurve.png │ ├── remote_mapping_files1.png │ ├── remote_mapping_files2.png │ ├── remote_mapping_files3.png │ ├── shotgun_analysis_gn_ec_summary.png │ ├── shotgun_analysis_gn_ec_summary_legend.png │ ├── shotgun_analysis_gn_pcoa.png │ ├── sink_predictions_pie_NICU_BabyBedside.png │ ├── stop_instance.png │ ├── taxheatmap.png │ ├── time_comparisons1.png │ ├── time_comparisons2.png │ ├── time_comparisons3.png │ └── tree.png ├── index.rst ├── install │ ├── alternative.rst │ ├── index.rst │ ├── install.rst │ ├── qiime_config.rst │ ├── upgrade.rst │ ├── virtual_box.rst │ └── vm_ec2.rst ├── scripts │ ├── add_alpha_to_mapping_file.rst │ ├── add_qiime_labels.rst │ ├── adjust_seq_orientation.rst │ ├── align_seqs.rst │ ├── alpha_diversity.rst │ ├── alpha_rarefaction.rst │ ├── ampliconnoise.rst │ ├── assign_taxonomy.rst │ ├── beta_diversity.rst │ ├── beta_diversity_through_plots.rst │ ├── beta_significance.rst │ ├── blast_wrapper.rst │ ├── categorized_dist_scatterplot.rst │ ├── clean_raxml_parsimony_tree.rst │ ├── cluster_quality.rst │ ├── collapse_samples.rst │ ├── collate_alpha.rst │ ├── compare_alpha_diversity.rst │ ├── compare_categories.rst │ ├── compare_distance_matrices.rst │ ├── compare_taxa_summaries.rst │ ├── compare_trajectories.rst │ ├── compute_core_microbiome.rst │ ├── compute_taxonomy_ratios.rst │ ├── conditional_uncovered_probability.rst │ ├── consensus_tree.rst │ ├── convert_fastaqual_fastq.rst │ ├── core_diversity_analyses.rst │ ├── count_seqs.rst │ ├── cytoscape_usage.rst │ ├── demultiplex_fasta.rst │ ├── denoise_wrapper.rst │ ├── denoiser.rst │ ├── denoiser_preprocess.rst │ ├── denoiser_worker.rst │ ├── detrend.rst │ ├── differential_abundance.rst │ ├── dissimilarity_mtx_stats.rst │ ├── distance_matrix_from_mapping.rst │ ├── estimate_observation_richness.rst │ ├── exclude_seqs_by_blast.rst │ ├── extract_barcodes.rst │ ├── extract_reads_from_interleaved_file.rst │ ├── extract_seqs_by_sample_id.rst │ ├── filter_alignment.rst │ ├── filter_distance_matrix.rst │ ├── filter_fasta.rst │ ├── filter_otus_by_sample.rst │ ├── filter_otus_from_otu_table.rst │ ├── filter_samples_from_otu_table.rst │ ├── filter_taxa_from_otu_table.rst │ ├── filter_tree.rst │ ├── fix_arb_fasta.rst │ ├── group_significance.rst │ ├── identify_chimeric_seqs.rst │ ├── identify_missing_files.rst │ ├── identify_paired_differences.rst │ ├── index.rst │ ├── inflate_denoiser_output.rst │ ├── jackknifed_beta_diversity.rst │ ├── join_paired_ends.rst │ ├── load_remote_mapping_file.rst │ ├── make_2d_plots.rst │ ├── make_bipartite_network.rst │ ├── make_bootstrapped_tree.rst │ ├── make_distance_boxplots.rst │ ├── make_distance_comparison_plots.rst │ ├── make_fastq.rst │ ├── make_library_id_lists.rst │ ├── make_otu_heatmap.rst │ ├── make_otu_network.rst │ ├── make_otu_table.rst │ ├── make_per_library_sff.rst │ ├── make_phylogeny.rst │ ├── make_prefs_file.rst │ ├── make_qiime_py_file.rst │ ├── make_rarefaction_plots.rst │ ├── make_tep.rst │ ├── map_reads_to_reference.rst │ ├── merge_mapping_files.rst │ ├── merge_otu_maps.rst │ ├── merge_otu_tables.rst │ ├── multiple_extract_barcodes.rst │ ├── multiple_join_paired_ends.rst │ ├── multiple_rarefactions.rst │ ├── multiple_rarefactions_even_depth.rst │ ├── multiple_split_libraries_fastq.rst │ ├── neighbor_joining.rst │ ├── nmds.rst │ ├── normalize_table.rst │ ├── observation_metadata_correlation.rst │ ├── parallel_align_seqs_pynast.rst │ ├── parallel_alpha_diversity.rst │ ├── parallel_assign_taxonomy_blast.rst │ ├── parallel_assign_taxonomy_rdp.rst │ ├── parallel_assign_taxonomy_uclust.rst │ ├── parallel_beta_diversity.rst │ ├── parallel_blast.rst │ ├── parallel_identify_chimeric_seqs.rst │ ├── parallel_map_reads_to_reference.rst │ ├── parallel_merge_otu_tables.rst │ ├── parallel_multiple_rarefactions.rst │ ├── parallel_pick_otus_blast.rst │ ├── parallel_pick_otus_sortmerna.rst │ ├── parallel_pick_otus_trie.rst │ ├── parallel_pick_otus_uclust_ref.rst │ ├── parallel_pick_otus_usearch61_ref.rst │ ├── pick_closed_reference_otus.rst │ ├── pick_de_novo_otus.rst │ ├── pick_open_reference_otus.rst │ ├── pick_otus.rst │ ├── pick_rep_set.rst │ ├── plot_rank_abundance_graph.rst │ ├── plot_semivariogram.rst │ ├── plot_taxa_summary.rst │ ├── poller.rst │ ├── principal_coordinates.rst │ ├── print_metadata_stats.rst │ ├── print_qiime_config.rst │ ├── process_iseq.rst │ ├── process_qseq.rst │ ├── process_sff.rst │ ├── quality_scores_plot.rst │ ├── relatedness.rst │ ├── shared_phylotypes.rst │ ├── simsam.rst │ ├── single_rarefaction.rst │ ├── sort_otu_table.rst │ ├── split_libraries.rst │ ├── split_libraries_fastq.rst │ ├── split_libraries_lea_seq.rst │ ├── split_otu_table.rst │ ├── split_otu_table_by_taxonomy.rst │ ├── split_sequence_file_on_sample_ids.rst │ ├── start_parallel_jobs.rst │ ├── start_parallel_jobs_sc.rst │ ├── start_parallel_jobs_slurm.rst │ ├── start_parallel_jobs_torque.rst │ ├── subsample_fasta.rst │ ├── summarize_taxa.rst │ ├── summarize_taxa_through_plots.rst │ ├── supervised_learning.rst │ ├── transform_coordinate_matrices.rst │ ├── tree_compare.rst │ ├── trflp_file_to_otu_table.rst │ ├── trim_sff_primers.rst │ ├── truncate_fasta_qual_files.rst │ ├── truncate_reverse_primer.rst │ ├── unweight_fasta.rst │ ├── upgma_cluster.rst │ ├── validate_demultiplexed_fasta.rst │ └── validate_mapping_file.rst └── tutorials │ ├── category_comparison.rst │ ├── chaining_otu_pickers.rst │ ├── chimera_checking.rst │ ├── creating_distance_comparison_plots.rst │ ├── denoising_454_data.rst │ ├── denoising_and_chimera_detection_usage_comparison.rst │ ├── distance_matrix_comparison.rst │ ├── extracting_barcodes_from_fastq_data.rst │ ├── filtering_contamination_otus.rst │ ├── fungal_its_analysis.rst │ ├── illumina_overview_tutorial.rst │ ├── index.rst │ ├── making_cytoscape_networks.rst │ ├── metadata_description.rst │ ├── open_reference_illumina_processing.rst │ ├── otu_picking.rst │ ├── parallel_qiime.rst │ ├── predicting_mislabeled_samples.rst │ ├── processing_18S_data.rst │ ├── processing_illumina_data.rst │ ├── procrustes_analysis.rst │ ├── remote_mapping_files.rst │ ├── retraining_rdp.rst │ ├── rtax.rst │ ├── running_supervised_learning.rst │ ├── shotgun_analysis.rst │ ├── source_tracking.rst │ ├── taxa_summary_comparison.rst │ ├── tutorial.rst │ ├── unix_commands.rst │ ├── usearch_quality_filter.rst │ ├── working_with_aws.rst │ └── working_with_biom_tables.rst ├── examples └── ipynb │ ├── Fungal-ITS-analysis.ipynb │ ├── illumina_overview_tutorial.ipynb │ └── illumina_overview_tutorial_workshop_template.ipynb ├── qiime ├── __init__.py ├── add_alpha_to_mapping_file.py ├── add_qiime_labels.py ├── adjust_seq_orientation.py ├── align_seqs.py ├── alpha_diversity.py ├── assign_taxonomy.py ├── barcode.py ├── beta_diversity.py ├── beta_metrics.py ├── biplots.py ├── categorized_dist_scatterplot.py ├── check_id_map.py ├── clean_raxml_parsimony_tree.py ├── cluster_quality.py ├── collate_alpha.py ├── colors.py ├── compare_alpha_diversity.py ├── compare_categories.py ├── compare_distance_matrices.py ├── compare_taxa_summaries.py ├── compare_trajectories.py ├── compute_taxonomy_ratios.py ├── convert_fastaqual_fastq.py ├── core_microbiome.py ├── demultiplex_fasta.py ├── denoise_wrapper.py ├── denoiser │ ├── __init__.py │ ├── cluster_utils.py │ ├── denoise_postprocess.py │ ├── denoise_worker.py │ ├── flowgram_clustering.py │ ├── flowgram_filter.py │ ├── make_cluster_jobs.py │ ├── preprocess.py │ └── utils.py ├── detrend.py ├── differential_abundance.py ├── distance_matrix_from_mapping.py ├── estimate_observation_richness.py ├── exclude_seqs_by_blast.py ├── extract_barcodes.py ├── filter.py ├── filter_alignment.py ├── filter_otus_by_sample.py ├── format.py ├── golay.py ├── group.py ├── hamming.py ├── hierarchical_cluster.py ├── identify_chimeric_seqs.py ├── join_paired_ends.py ├── make_2d_plots.py ├── make_bipartite_network.py ├── make_bootstrapped_tree.py ├── make_distance_boxplots.py ├── make_fastq.py ├── make_library_id_lists.py ├── make_otu_heatmap.py ├── make_otu_network.py ├── make_otu_table.py ├── make_per_library_sff.py ├── make_phylogeny.py ├── make_rarefaction_plots.py ├── map_reads_to_reference.py ├── nmds.py ├── normalize_table.py ├── otu_significance.py ├── parallel │ ├── __init__.py │ ├── align_seqs.py │ ├── alpha_diversity.py │ ├── assign_taxonomy.py │ ├── beta_diversity.py │ ├── blast.py │ ├── identify_chimeric_seqs.py │ ├── map_reads_to_reference.py │ ├── merge_otus.py │ ├── multiple_rarefactions.py │ ├── pick_otus.py │ ├── poller.py │ └── util.py ├── parse.py ├── pick_otus.py ├── pick_rep_set.py ├── plot_rank_abundance_graph.py ├── plot_semivariogram.py ├── plot_taxa_summary.py ├── principal_coordinates.py ├── process_sff.py ├── pycogent_backports │ ├── __init__.py │ └── fastq.py ├── quality_scores_plot.py ├── rarefaction.py ├── relatedness_library.py ├── remote.py ├── shared_phylotypes.py ├── simsam.py ├── sort.py ├── split.py ├── split_libraries.py ├── split_libraries_fastq.py ├── split_libraries_lea_seq.py ├── stats.py ├── summarize_taxa.py ├── supervised_learning.py ├── support_files │ ├── R │ │ ├── CSS.r │ │ ├── DESeq2.r │ │ ├── DESeq2_nbinom.r │ │ ├── adonis.r │ │ ├── dbrda.r │ │ ├── detrend.r │ │ ├── detrend_util.r │ │ ├── fitZIG.r │ │ ├── loaddata.r │ │ ├── morans_i.r │ │ ├── mrpp.r │ │ ├── permdisp.r │ │ ├── randomforests.r │ │ ├── randomforests_util.r │ │ └── util.r │ ├── css │ │ └── qiime_style.css │ ├── denoiser │ │ ├── CHANGELOG │ │ ├── CREDITS │ │ ├── Data │ │ │ ├── FLX_error_profile.dat │ │ │ ├── Titanium_error_profile.dat │ │ │ └── probabilities.txt │ │ ├── FlowgramAlignment │ │ │ ├── ADPCombinators.lhs │ │ │ ├── FlowgramAli_4frame.lhs │ │ │ ├── FlowgramUtils.lhs │ │ │ └── Makefile │ │ └── TestData │ │ │ ├── denoiser_test_set.sff.txt │ │ │ ├── test_flow_file.dat │ │ │ ├── test_set_seqs.fna │ │ │ └── tiny_test.sff.txt │ ├── images │ │ └── qiime_header.png │ ├── js │ │ ├── histograms.js │ │ ├── jquery.js │ │ ├── jquery.tablednd_0_5.js │ │ ├── otu_count_display.js │ │ └── overlib.js │ ├── qiime_config │ └── test_js │ │ └── test_otu_count_display.html ├── test.py ├── transform_coordinate_matrices.py ├── tree_compare.py ├── trim_sff_primers.py ├── truncate_fasta_qual_files.py ├── truncate_reverse_primer.py ├── util.py ├── validate_demultiplexed_fasta.py └── workflow │ ├── __init__.py │ ├── ampliconnoise.py │ ├── core_diversity_analyses.py │ ├── downstream.py │ ├── pick_open_reference_otus.py │ ├── preprocess.py │ ├── upstream.py │ └── util.py ├── qiime_test_data ├── __init__.py ├── add_alpha_to_mapping_file │ ├── adiv_pd.txt │ ├── chao1.txt │ ├── mapping.txt │ └── shannon.txt ├── add_qiime_labels │ ├── example_mapping.txt │ └── fasta_dir │ │ ├── seqs1.fna │ │ └── seqs2.fna ├── adjust_seq_orientation │ ├── seqs.fna │ └── seqs_rc.fna ├── align_seqs │ ├── core_set_aligned.fasta.imputed │ ├── infernal_aligned │ │ ├── unaligned_aligned.fasta │ │ └── unaligned_log.txt │ ├── muscle_alignment │ │ ├── unaligned_aligned.fasta │ │ └── unaligned_log.txt │ ├── pynast_aligned │ │ ├── unaligned_aligned.fasta │ │ ├── unaligned_failures.fasta │ │ └── unaligned_log.txt │ ├── seed.16s.reference_model.sto │ └── unaligned.fna ├── alpha_diversity │ ├── otu_table.biom │ ├── otu_tables │ │ ├── otu_table_1.biom │ │ ├── otu_table_2.biom │ │ └── otu_table_3.biom │ └── rep_set.tre ├── alpha_rarefaction │ ├── Fasting_Map.txt │ ├── otu_table.biom │ └── rep_set.tre ├── ampliconnoise │ ├── Fasting_Example.sff.txt │ └── Fasting_Map.txt ├── assign_taxonomy │ ├── id_to_taxonomy.txt │ ├── mothur_id_to_taxonomy.txt │ ├── mothur_ref_seq_set.fna │ ├── mothur_repr_set_seqs.fasta │ ├── read_1.seqs.fna │ ├── read_2.seqs.fna │ ├── ref_seq_set.fna │ ├── repr_set_seqs.fasta │ ├── rtax_id_to_taxonomy.txt │ ├── rtax_ref_seq_set.fna │ ├── rtax_repr_set_seqs.fasta │ └── uclust_assigned_taxonomy │ │ ├── repr_set_seqs_tax_assignments.log │ │ └── repr_set_seqs_tax_assignments.txt ├── beta_diversity │ ├── otu_table.biom │ ├── otu_tables │ │ ├── otu_table_1.biom │ │ ├── otu_table_2.biom │ │ └── otu_table_3.biom │ └── rep_set.tre ├── beta_diversity_through_plots │ ├── Fasting_Map.txt │ ├── otu_table.biom │ └── rep_set.tre ├── beta_significance │ ├── otu_table.biom │ └── rep_set.tre ├── blast_wrapper │ ├── inseqs.fasta │ └── refseqs.fasta ├── cluster_quality │ ├── Fasting_Map.txt │ ├── quality_dob.txt │ ├── quality_treatment.txt │ └── weighted_unifrac_otu_table.txt ├── collapse_samples │ ├── map.txt │ └── table.biom ├── collate_alpha │ └── alpha_div │ │ ├── alpha_rarefaction_101_1.txt │ │ ├── alpha_rarefaction_101_3.txt │ │ ├── alpha_rarefaction_101_7.txt │ │ ├── alpha_rarefaction_101_9.txt │ │ ├── alpha_rarefaction_10_1.txt │ │ ├── alpha_rarefaction_10_3.txt │ │ ├── alpha_rarefaction_10_7.txt │ │ ├── alpha_rarefaction_10_9.txt │ │ ├── alpha_rarefaction_114_1.txt │ │ ├── alpha_rarefaction_114_3.txt │ │ ├── alpha_rarefaction_114_7.txt │ │ ├── alpha_rarefaction_114_9.txt │ │ ├── alpha_rarefaction_127_1.txt │ │ ├── alpha_rarefaction_127_3.txt │ │ ├── alpha_rarefaction_127_7.txt │ │ ├── alpha_rarefaction_127_9.txt │ │ ├── alpha_rarefaction_140_1.txt │ │ ├── alpha_rarefaction_140_3.txt │ │ ├── alpha_rarefaction_140_7.txt │ │ ├── alpha_rarefaction_140_9.txt │ │ ├── alpha_rarefaction_23_1.txt │ │ ├── alpha_rarefaction_23_3.txt │ │ ├── alpha_rarefaction_23_7.txt │ │ ├── alpha_rarefaction_23_9.txt │ │ ├── alpha_rarefaction_36_1.txt │ │ ├── alpha_rarefaction_36_3.txt │ │ ├── alpha_rarefaction_36_7.txt │ │ ├── alpha_rarefaction_36_9.txt │ │ ├── alpha_rarefaction_49_1.txt │ │ ├── alpha_rarefaction_49_3.txt │ │ ├── alpha_rarefaction_49_7.txt │ │ ├── alpha_rarefaction_49_9.txt │ │ ├── alpha_rarefaction_62_1.txt │ │ ├── alpha_rarefaction_62_3.txt │ │ ├── alpha_rarefaction_62_7.txt │ │ ├── alpha_rarefaction_62_9.txt │ │ ├── alpha_rarefaction_75_1.txt │ │ ├── alpha_rarefaction_75_3.txt │ │ ├── alpha_rarefaction_75_7.txt │ │ ├── alpha_rarefaction_75_9.txt │ │ ├── alpha_rarefaction_88_1.txt │ │ ├── alpha_rarefaction_88_3.txt │ │ ├── alpha_rarefaction_88_7.txt │ │ └── alpha_rarefaction_88_9.txt ├── compare_alpha_diversity │ ├── PD_whole_tree.txt │ └── mapping.txt ├── compare_categories │ ├── Fasting_Map.txt │ └── unweighted_unifrac_dm.txt ├── compare_distance_matrices │ ├── PH_dm.txt │ ├── unweighted_unifrac_dm.txt │ ├── unweighted_unifrac_even100_dm.txt │ ├── weighted_unifrac_dm.txt │ └── weighted_unifrac_even100_dm.txt ├── compare_taxa_summaries │ ├── sample_id_map.txt │ ├── ts_rdp_0.60.txt │ ├── ts_rdp_0.60_renamed.txt │ └── ts_rdp_0.80.txt ├── compare_trajectories │ ├── map.txt │ └── pcoa_res.txt ├── compute_core_microbiome │ ├── map.txt │ ├── otu_table.biom │ └── otu_table_core_50.biom ├── compute_taxonomy_ratios │ ├── map.txt │ └── table.biom.gz ├── conditional_uncovered_probability │ └── otu_table.biom ├── consensus_tree │ └── jackknifed_trees │ │ ├── bs1.tre │ │ ├── bs2.tre │ │ ├── bs3.tre │ │ └── bs4.tre ├── convert_fastaqual_fastq │ ├── seqs.fastq │ ├── seqs.fna │ └── seqs.qual ├── core_diversity_analyses │ ├── map.txt │ ├── otu_table.biom │ └── rep_set.tre ├── count_seqs │ ├── in.fasta │ ├── in1.fasta │ ├── in2.fasta │ └── in2.fastq ├── demultiplex_fasta │ ├── .DS_Store │ ├── 1.TCA.454Reads.fna │ ├── 1.TCA.454Reads.qual │ ├── 2.TCA.454Reads.fna │ ├── 2.TCA.454Reads.qual │ ├── Mapping_File1.txt │ ├── Mapping_File2.txt │ ├── Mapping_File_8bp_barcodes.txt │ ├── Mapping_File_golay.txt │ └── Mapping_File_run_prefix.txt ├── denoiser_preprocess │ ├── Fasting_Example.sff.txt │ ├── preproc_out │ │ ├── prefix_dereplicated.fasta │ │ ├── prefix_dereplicated.sff.txt │ │ └── prefix_mapping.txt │ └── seqs.fna ├── differential_abundance │ ├── map.txt │ ├── otu_table.biom │ └── otu_tables │ │ ├── otu_table_1.biom │ │ └── otu_table_2.biom ├── dissimilarity_mtx_stats │ └── dists │ │ ├── unweighted_unifrac_dm.txt │ │ └── weighted_unifrac_dm.txt ├── distance_matrix_from_mapping │ ├── Fasting_Map.txt │ ├── lat_long.txt │ └── map_distance_matrix.txt ├── estimate_observation_richness │ └── otu_table.biom ├── exclude_seqs_by_blast │ ├── ref_seq_set.fna │ └── repr_set_seqs.fasta ├── extract_reads_from_interleaved_file │ └── reads_to_extract.fastq ├── extract_seqs_by_sample_id │ ├── inseqs.fasta │ └── map.txt ├── filter_alignment │ ├── filtered_alignment_gap_95 │ │ └── seqs_rep_set_aligned_pfiltered.fasta │ └── seqs_rep_set_aligned.fasta ├── filter_distance_matrix │ ├── Fasting_Map.txt │ ├── dm.txt │ ├── otu_table.biom │ └── sample_id_list.txt ├── filter_fasta │ ├── chimeric_seqs.txt │ ├── inseqs.fasta │ ├── inseqs.fastq │ ├── map.txt │ ├── otu_map.txt │ ├── otu_table.biom │ ├── seqs_to_keep.txt │ └── sl_inseqs.fasta ├── filter_otus_by_sample │ ├── seqs.fna │ └── seqs_otus.txt ├── filter_otus_from_otu_table │ ├── chimeric_otus.txt │ └── otu_table.biom ├── filter_samples_from_otu_table │ ├── ids.txt │ ├── map.txt │ └── otu_table.biom ├── filter_taxa_from_otu_table │ └── otu_table.biom ├── filter_tree │ ├── fast_f.fna │ ├── pruned_fasta.tre │ ├── rep_seqs.tre │ └── tips_to_keep.txt ├── fix_arb_fasta │ └── arb.fasta ├── group_significance │ ├── btt_ocs.txt │ ├── gtest_ocs.txt │ ├── kw_ocs.txt │ ├── map.txt │ ├── map_overlapping.txt │ ├── otu_table.biom │ └── tt_ocs.txt ├── identify_chimeric_seqs │ ├── chimeric_seqs.txt │ ├── formatdb.log │ ├── ref_seq_set.fna │ ├── ref_seq_set_aligned.fasta │ ├── ref_seq_set_aligned.fasta.cidx │ ├── ref_sequences.fasta │ ├── repr_set_seqs.fasta │ ├── repr_set_seqs_aligned.fasta │ ├── seqs.fna │ └── taxonomy_assignment.txt ├── identify_missing_files │ └── ALIGN_BQ7_ │ │ ├── a.txt │ │ ├── b.txt │ │ └── expected_out_files.txt ├── identify_paired_differences │ ├── map.txt │ └── otu_table.biom ├── inflate_denoiser_output │ ├── centroids.fasta │ ├── centroids1.fasta │ ├── centroids2.fasta │ ├── combined │ │ ├── Fasting_Example.sff │ │ ├── Fasting_Example_1st_half.fna │ │ ├── Fasting_Example_1st_half.qual │ │ ├── Fasting_Example_1st_half.sff │ │ ├── Fasting_Example_1st_half.sff.txt │ │ ├── Fasting_Example_2nd_half.fna │ │ ├── Fasting_Example_2nd_half.qual │ │ ├── Fasting_Example_2nd_half.sff │ │ ├── Fasting_Example_2nd_half.sff.txt │ │ ├── Fasting_Map.txt │ │ ├── denoised_1st_half │ │ │ ├── centroids.fasta │ │ │ ├── denoised_clusters.txt │ │ │ ├── denoised_seqs.fasta │ │ │ ├── denoiser.log │ │ │ ├── denoiser_mapping.txt │ │ │ ├── prefix_dereplicated.fasta │ │ │ ├── prefix_dereplicated.sff.txt │ │ │ ├── prefix_mapping.txt │ │ │ └── singletons.fasta │ │ ├── denoised_2nd_half │ │ │ ├── centroids.fasta │ │ │ ├── denoised_clusters.txt │ │ │ ├── denoised_seqs.fasta │ │ │ ├── denoiser.log │ │ │ ├── denoiser_mapping.txt │ │ │ ├── prefix_dereplicated.fasta │ │ │ ├── prefix_dereplicated.sff.txt │ │ │ ├── prefix_mapping.txt │ │ │ └── singletons.fasta │ │ ├── denoised_combined.fna │ │ ├── seq_ids.txt │ │ ├── seq_ids_1st_half.txt │ │ ├── seq_ids_2nd_half.txt │ │ ├── split_libraries_output_1st_half │ │ │ ├── histograms.txt │ │ │ ├── seqs.fna │ │ │ └── split_library_log.txt │ │ └── split_libraries_output_2nd_half │ │ │ ├── histograms.txt │ │ │ ├── seqs.fna │ │ │ └── split_library_log.txt │ ├── denoiser_mapping.txt │ ├── denoiser_mapping1.txt │ ├── denoiser_mapping2.txt │ ├── seqs.fna │ ├── seqs1.fna │ ├── seqs2.fna │ ├── singletons.fasta │ ├── singletons1.fasta │ └── singletons2.fasta ├── jackknifed_beta_diversity │ ├── Fasting_Map.txt │ ├── otu_table.biom │ └── rep_set.tre ├── join_paired_ends │ ├── barcodes.fastq │ ├── forward_reads.fastq │ └── reverse_reads.fastq ├── make_2d_plots │ ├── 20121016150418fvEtn34Xui5ZGvKhQnhI │ │ ├── 201210161504183YSZLtkVlW0WiMeW1hw5 │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ │ ├── 20121016150418yGn50OalsFKxVgdCPKHV │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ │ ├── 20121016150419dazkbiLaQpqTxIbSz2HR │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ │ ├── 20121016150419o1Rv7IQSdPYPmFSLR0Mp │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ │ ├── 20121016150420RH7QimybYhiSMYayO5qF │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ │ └── 20121016150420aDFutSkIU91iUxOKfLer │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ ├── 20121016150441FneURRPQ3TIvFUySfGZg │ │ └── 20121016150441YgWyD9TKTvkxolKSTB0D │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ ├── 20121016150454Ll4EIvhlOtME3ZB24iOE │ │ ├── 20121016150454Dt11u49Ld4DFd05HgbN3 │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ │ ├── 201210161504559CaeyTXq6cvBD72kXQU7 │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ │ ├── 20121016150455PbRxRwl0uQp91000stgB │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ │ ├── 20121016150456FeeuBdhygXkuGgrGeVzn │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ │ ├── 20121016150456os1oHWmcH5xal2tYRcnD │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ │ ├── 20121016150457fTuYkZLKssYEoPRIrkmK │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ │ └── 20121016150457nZgflu6OEO64tF7xoRFG │ │ │ ├── scree_plot.eps.gz │ │ │ └── scree_plot.png │ ├── 201210161505024UcKASqirfxUIpDmlyWE │ │ ├── 20121016150502RVgilhcBleFnMWi6ndGG │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ │ ├── 20121016150503WA6HUI4W4nbtC0YGS19A │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ │ ├── 20121016150503p2Tq2Bnf0PVHQmupiGMk │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ │ ├── 20121016150504C6EdpKyfMKYuMtZGiGLO │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ │ ├── 20121016150504Fogr95nWRxpY1CPPPZOM │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ │ └── 20121016150505VGWEdylGluXosgtfR0I1 │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ ├── 20121016150511ED4PikD6rsXgDMHLYmPo │ │ ├── 20121016150511365u20ZGT5vgLoHQmet0 │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ │ └── 20121016150512GIx3mmRLLlrshskqIioX │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ ├── 20121016150521AsYMBmMaRBb3IknrAMmc │ │ └── 20121016150521b2Dag0vPefYGgCaKv9iX │ │ │ ├── PC1_vs_PC2_plot.png │ │ │ ├── PC1_vs_PC3_plot.png │ │ │ ├── PC1vsPC2plot.eps.gz │ │ │ ├── PC1vsPC3plot.eps.gz │ │ │ ├── PC3_vs_PC2_plot.png │ │ │ └── PC3vsPC2plot.eps.gz │ ├── Fasting_Map.txt │ ├── _2D_PCoA_plots.html │ ├── js │ │ └── overlib.js │ ├── pcoa │ │ ├── pcoa_unweighted_unifrac_rarefaction_100_0.txt │ │ ├── pcoa_unweighted_unifrac_rarefaction_100_1.txt │ │ ├── pcoa_unweighted_unifrac_rarefaction_100_2.txt │ │ ├── pcoa_unweighted_unifrac_rarefaction_100_3.txt │ │ ├── pcoa_unweighted_unifrac_rarefaction_100_4.txt │ │ ├── pcoa_unweighted_unifrac_rarefaction_100_5.txt │ │ ├── pcoa_unweighted_unifrac_rarefaction_100_6.txt │ │ ├── pcoa_unweighted_unifrac_rarefaction_100_7.txt │ │ ├── pcoa_unweighted_unifrac_rarefaction_100_8.txt │ │ └── pcoa_unweighted_unifrac_rarefaction_100_9.txt │ ├── prefs.txt │ ├── unweighted_unifrac_pc.txt │ └── unweighted_unifrac_pc_2D_PCoA_plots.html ├── make_bipartite_network │ ├── mapping_file.txt │ └── otu_table.biom ├── make_bootstrapped_tree │ ├── jackknife_support.txt │ └── master_tree.tre ├── make_distance_boxplots │ ├── Fasting_Map.txt │ └── unweighted_unifrac_dm.txt ├── make_distance_comparison_plots │ ├── costello_timeseries_map.txt │ └── forearm_only_unweighted_unifrac_dm.txt ├── make_fastq │ ├── Fasting_Example.fna │ ├── Fasting_Example.qual │ ├── Fasting_Map.txt │ ├── README.txt │ ├── histograms.txt │ ├── seqs.fna │ ├── seqs.fna.fastq_example │ │ ├── PC.354.fastq │ │ ├── PC.355.fastq │ │ ├── PC.356.fastq │ │ ├── PC.481.fastq │ │ ├── PC.593.fastq │ │ ├── PC.607.fastq │ │ ├── PC.634.fastq │ │ ├── PC.635.fastq │ │ └── PC.636.fastq │ └── split_library_log.txt ├── make_otu_heatmap │ ├── mapping_file.txt │ ├── otu_table.biom │ └── rep_set.tre ├── make_otu_network │ ├── Fasting_Map.txt │ └── otu_table.biom ├── make_otu_table │ ├── chimeric_seqs.txt │ ├── mapping_file.txt │ ├── otu_map.txt │ ├── pynast_failures.fna │ └── tax_assignments.txt ├── make_phylogeny │ ├── aligned.fasta │ └── aligned.tre ├── make_prefs_file │ ├── mapping.txt │ └── taxa_level_3.txt ├── make_rarefaction_plots │ ├── Fasting_Map.txt │ ├── alpha_div_collated │ │ ├── PD_whole_tree.txt │ │ ├── chao1.txt │ │ └── observed_species.txt │ └── prefs.txt ├── make_tep │ ├── Fasting_Map.txt │ ├── make_tep_output │ │ ├── otu_table.jnlp │ │ └── otu_table.tep │ ├── otu_table.biom │ └── rep_set.tre ├── map_reads_to_reference │ ├── blat-nt_mapped │ │ ├── observation_map.txt │ │ ├── observation_table.biom │ │ ├── observation_table.log │ │ └── out.bl9 │ ├── blat_mapped │ │ ├── observation_map.txt │ │ ├── observation_table.biom │ │ ├── observation_table.log │ │ └── out.bl9 │ ├── bwa-short_mapped │ │ ├── bwa_raw_out.sai │ │ ├── bwa_raw_out.sam │ │ ├── observation_map.txt │ │ ├── observation_table.biom │ │ └── observation_table.log │ ├── bwa-sw_mapped │ │ ├── bwa_raw_out.sam │ │ ├── observation_map.txt │ │ ├── observation_table.biom │ │ └── observation_table.log │ ├── query_nt.fasta │ ├── refseqs_nt.fasta │ ├── refseqs_nt_md.txt │ ├── refseqs_pr.fasta │ ├── refseqs_pr_md.txt │ └── usearch_mapped │ │ ├── observation_map.txt │ │ ├── observation_table.biom │ │ ├── out.bl6 │ │ └── out.uc ├── merge_mapping_files │ ├── map_controls.txt │ └── map_fasting.txt ├── merge_otu_maps │ ├── fail.txt │ ├── otu_map1.txt │ ├── otu_map2.txt │ └── otu_map_fail.txt ├── merge_otu_tables │ ├── otu_table1.biom │ └── otu_table2.biom ├── multiple_extract_barcodes │ ├── input_files │ │ ├── unmatched1_R1_zz_sample.fastq │ │ ├── xxxx_R1_sample.fastq │ │ └── zzzz_R1_zz_sample.fastq.gz │ ├── input_folders │ │ ├── folder1 │ │ │ ├── xxxx_forward_sample.fastq │ │ │ └── xxxx_reverse_sample.fastq │ │ └── folder2 │ │ │ ├── xxxx_forward_sample.fastq │ │ │ └── xxxx_reverse_sample.fastq │ └── qiime_parameters.txt ├── multiple_join_paired_ends │ ├── input_files │ │ ├── unmatched1_R1_zz_sample.fastq │ │ ├── unmatched2_R2_zz_sample.fastq │ │ ├── xxxx_R1_sample.fastq │ │ ├── xxxx_R2_sample.fastq │ │ ├── zzzz_R1_zz_sample.fastq.gz │ │ └── zzzz_R2_zz_sample.fastq.gz │ ├── input_folders │ │ ├── folder1 │ │ │ ├── xxxx_barcode_sample.fastq │ │ │ ├── xxxx_forward_sample.fastq │ │ │ └── xxxx_reverse_sample.fastq │ │ └── folder2 │ │ │ ├── xxxx_barcode_sample.fastq │ │ │ ├── xxxx_forward_sample.fastq │ │ │ └── xxxx_reverse_sample.fastq │ └── qiime_parameters.txt ├── multiple_rarefactions │ └── otu_table.biom ├── multiple_rarefactions_even_depth │ └── otu_table.biom ├── multiple_split_libraries_fastq │ ├── input_files │ │ ├── unmatched1_R1_zz_sample.fastq │ │ ├── xxxx_R1_sample.fastq │ │ └── zzzz_R1_zz_sample.fastq.gz │ ├── input_folders │ │ ├── folder1 │ │ │ ├── xxxx_barcode_sample.fastq │ │ │ ├── xxxx_mapping_sample.txt │ │ │ └── xxxx_reads_sample.fastq │ │ └── folder2 │ │ │ ├── xxxx_barcode_sample.fastq │ │ │ ├── xxxx_mapping_sample.txt │ │ │ └── xxxx_reads_sample.fastq │ ├── input_folders_no_barcodes │ │ ├── sample1 │ │ │ └── xxxx_reads_sample.fastq │ │ └── sample2 │ │ │ └── xxxx_reads_sample.fastq │ └── qiime_parameters.txt ├── neighbor_joining │ ├── beta_div.txt │ └── beta_div_weighted_unifrac │ │ ├── weighted_unifrac_otu_table.txt │ │ ├── weighted_unifrac_otu_table_1.txt │ │ ├── weighted_unifrac_otu_table_2.txt │ │ └── weighted_unifrac_otu_table_3.txt ├── nmds │ ├── beta_div.txt │ └── beta_div_weighted_unifrac │ │ ├── weighted_unifrac_otu_table.txt │ │ ├── weighted_unifrac_otu_table_1.txt │ │ ├── weighted_unifrac_otu_table_2.txt │ │ └── weighted_unifrac_otu_table_3.txt ├── normalize_table │ ├── otu_table.biom │ └── otu_tables │ │ ├── otu_table_1.biom │ │ └── otu_table_2.biom ├── observation_metadata_correlation │ ├── map.txt │ └── otu_table.biom ├── parallel_align_seqs_pynast │ ├── inseqs.fasta │ └── jobs │ │ ├── ALIGN_yw7_0 │ │ ├── ALIGN_yw7_1 │ │ └── ALIGN_yw7_2 ├── parallel_alpha_diversity │ ├── rarefied_otu_tables │ │ ├── rarefaction_100_0.biom │ │ ├── rarefaction_100_1.biom │ │ ├── rarefaction_100_2.biom │ │ ├── rarefaction_100_3.biom │ │ ├── rarefaction_100_4.biom │ │ ├── rarefaction_100_5.biom │ │ ├── rarefaction_100_6.biom │ │ ├── rarefaction_100_7.biom │ │ ├── rarefaction_100_8.biom │ │ └── rarefaction_100_9.biom │ └── rep_set.tre ├── parallel_assign_taxonomy_blast │ ├── id_to_tax.txt │ ├── inseqs.fasta │ └── refseqs.fasta ├── parallel_assign_taxonomy_rdp │ ├── inseqs.fasta │ └── jobs │ │ ├── RDP_IUbHy_0 │ │ ├── RDP_IUbHy_1 │ │ └── RDP_IUbHy_2 ├── parallel_assign_taxonomy_uclust │ └── inseqs.fasta ├── parallel_beta_diversity │ ├── jobs │ │ ├── BDIV_XAF0_0 │ │ ├── BDIV_XAF0_1 │ │ └── BDIV_XAF0_2 │ ├── otu_table.biom │ ├── rarefied_otu_tables │ │ ├── rarefaction_100_0.biom │ │ ├── rarefaction_100_1.biom │ │ ├── rarefaction_100_2.biom │ │ ├── rarefaction_100_3.biom │ │ ├── rarefaction_100_4.biom │ │ ├── rarefaction_100_5.biom │ │ ├── rarefaction_100_6.biom │ │ ├── rarefaction_100_7.biom │ │ ├── rarefaction_100_8.biom │ │ └── rarefaction_100_9.biom │ └── rep_set.tre ├── parallel_blast │ ├── inseqs.fasta │ ├── jobs │ │ ├── BLAST_bxw_0 │ │ ├── BLAST_bxw_1 │ │ ├── BLAST_bxw_2 │ │ ├── BLAST_fCy_0 │ │ ├── BLAST_fCy_1 │ │ ├── BLAST_fCy_2 │ │ ├── BLAST_pru_0 │ │ ├── BLAST_pru_1 │ │ └── BLAST_pru_2 │ └── refseqs.fasta ├── parallel_identify_chimeric_seqs │ ├── cs_refseqs_aligned.fasta │ ├── id_to_tax.txt │ ├── inseqs.fasta │ ├── inseqs_aligned.fasta │ └── refseqs.fasta ├── parallel_map_reads_to_reference │ ├── query_nt.fasta │ ├── refseqs_nt.fasta │ ├── refseqs_nt_md.txt │ ├── refseqs_pr.fasta │ └── refseqs_pr_md.txt ├── parallel_merge_otu_tables │ ├── foo │ │ └── merged │ │ │ ├── MOTU_BxH1_ │ │ │ ├── 0.biom │ │ │ ├── 0.biom.poll │ │ │ ├── 1.biom │ │ │ ├── 1.biom.poll │ │ │ └── 2.biom.poll │ │ │ ├── merged.biom │ │ │ └── parallel_merge_otus.log │ ├── t1.biom │ ├── t2.biom │ ├── t3.biom │ └── t4.biom ├── parallel_multiple_rarefactions │ ├── jobs │ │ ├── RARIF_7dA_0 │ │ ├── RARIF_7dA_1 │ │ ├── RARIF_7dA_2 │ │ ├── RARIF_Tul_0 │ │ ├── RARIF_Tul_1 │ │ └── RARIF_Tul_2 │ └── otu_table.biom ├── parallel_pick_otus_blast │ ├── refseqs.fna │ └── seqs.fna ├── parallel_pick_otus_sortmerna │ ├── refseqs.fna │ └── seqs.fna ├── parallel_pick_otus_trie │ └── seqs.fna ├── parallel_pick_otus_uclust_ref │ ├── refseqs.fna │ └── seqs.fna ├── parallel_pick_otus_usearch61_ref │ ├── refseqs.fna │ └── seqs.fna ├── pick_closed_reference_otus │ ├── refseqs.fna │ ├── seqs.fna │ ├── sortmerna_params.txt │ ├── taxa.txt │ ├── usearch5.2_params.txt │ └── usearch_params.txt ├── pick_de_novo_otus │ ├── seqs.fna │ ├── sumaclust_params.txt │ └── swarm_params.txt ├── pick_open_reference_otus │ ├── map.txt │ ├── refseqs.fna │ ├── seqs1.fna │ ├── seqs2.fna │ ├── ucrss_params.txt │ └── ucrss_smr_suma_params.txt ├── pick_otus │ ├── refseqs.fasta │ ├── refseqs.fasta.log │ ├── refseqs.fasta.nhr │ ├── refseqs.fasta.nin │ ├── refseqs.fasta.nsd │ ├── refseqs.fasta.nsi │ ├── refseqs.fasta.nsq │ ├── seqs.aligned.fna │ ├── seqs.fna │ └── uclust_ref_picked_otus │ │ ├── seqs_clusters.uc │ │ ├── seqs_failures.txt │ │ ├── seqs_otus.log │ │ └── seqs_otus.txt ├── pick_rep_set │ ├── refseqs.fasta │ ├── seqs.fna │ └── seqs_otus.txt ├── plot_rank_abundance_graph │ ├── all_plot.eps_log.txt │ ├── multi_plot.pdf_log.txt │ ├── otu_table.biom │ └── single_plot.pdf_log.txt ├── plot_semivariogram │ ├── Fasting_Map.txt │ ├── categories_legend.eps │ ├── distance.txt │ ├── time_dm.txt │ ├── unifrac.txt │ └── unweighted_unifrac_dm.txt ├── plot_taxa_summary │ ├── class.txt │ ├── family.txt │ ├── genus.txt │ ├── order.txt │ └── phylum.txt ├── poller │ ├── clean_up.txt │ ├── file1.txt │ ├── file2.txt │ ├── poller_test_completed.txt │ └── run_complete.txt ├── principal_coordinates │ ├── beta_div.txt │ └── beta_div_weighted_unifrac │ │ ├── weighted_unifrac_otu_table.txt │ │ ├── weighted_unifrac_otu_table_1.txt │ │ ├── weighted_unifrac_otu_table_2.txt │ │ └── weighted_unifrac_otu_table_3.txt ├── print_metadata_stats │ └── mapping.txt ├── quality_scores_plot │ ├── .DS_Store │ └── seqs.qual ├── relatedness │ ├── group1_otus.txt │ └── reference.tre ├── shared_phylotypes │ ├── otu_table.biom │ └── rarefied_otu_tables │ │ ├── rarefaction_100_0.biom │ │ ├── rarefaction_100_1.biom │ │ ├── rarefaction_100_2.biom │ │ ├── rarefaction_100_3.biom │ │ ├── rarefaction_100_4.biom │ │ ├── rarefaction_100_5.biom │ │ ├── rarefaction_100_6.biom │ │ ├── rarefaction_100_7.biom │ │ ├── rarefaction_100_8.biom │ │ └── rarefaction_100_9.biom ├── simsam │ ├── map.txt │ ├── otu_table.biom │ └── rep_set.tre ├── single_rarefaction │ └── otu_table.biom ├── sort_otu_table │ ├── Fasting_Map.txt │ ├── otu_table.biom │ └── sample_id_list.txt ├── split_libraries │ ├── 1.TCA.454Reads.fna │ ├── 1.TCA.454Reads.qual │ ├── 2.TCA.454Reads.fna │ ├── 2.TCA.454Reads.qual │ ├── Combined_seqs.fna │ ├── Mapping_File.txt │ ├── Mapping_File1.txt │ ├── Mapping_File2.txt │ ├── Mapping_File_8bp_barcodes.txt │ └── Mapping_File_reverse_primer.txt ├── split_libraries_fastq │ ├── lane1_barcode.fastq.gz │ ├── lane1_read1.fastq.gz │ ├── lane2_barcode.fastq.gz │ ├── lane2_read1.fastq.gz │ └── map.txt ├── split_libraries_lea_seq │ ├── fwd_read.fq │ ├── map.txt │ └── rev_read.fq ├── split_otu_table │ ├── Fasting_Map.txt │ └── otu_table.biom ├── split_otu_table_by_taxonomy │ └── otu_table.biom ├── split_sequence_file_on_sample_ids │ ├── seqs.fastq │ └── seqs.fna ├── start_parallel_jobs │ └── test_jobs.txt ├── start_parallel_jobs_sc │ └── test_jobs.txt ├── start_parallel_jobs_torque │ └── test_jobs.txt ├── subsample_fasta │ └── seqs.fna ├── summarize_taxa │ ├── Fasting_Map.txt │ └── otu_table.biom ├── summarize_taxa_through_plots │ ├── Fasting_Map.txt │ └── otu_table.biom ├── supervised_learning │ ├── Fasting_Map.txt │ ├── otu_table.biom │ ├── rarefied_tables │ │ ├── rarefaction_100_0.biom │ │ ├── rarefaction_100_1.biom │ │ ├── rarefaction_100_2.biom │ │ ├── rarefaction_100_3.biom │ │ ├── rarefaction_100_4.biom │ │ ├── rarefaction_100_5.biom │ │ ├── rarefaction_100_6.biom │ │ ├── rarefaction_100_7.biom │ │ ├── rarefaction_100_8.biom │ │ └── rarefaction_100_9.biom │ ├── sl_cv10_sweep.txt │ ├── sl_oob_sweep.txt │ └── sl_rarefied_tables_oob │ │ ├── sl_rarefaction_100_0_Treatment │ │ ├── confusion_matrix.txt │ │ ├── cv_probabilities.txt │ │ ├── feature_importance_scores.txt │ │ ├── mislabeling.txt │ │ └── summary.txt │ │ ├── sl_rarefaction_100_1_Treatment │ │ ├── confusion_matrix.txt │ │ ├── cv_probabilities.txt │ │ ├── feature_importance_scores.txt │ │ ├── mislabeling.txt │ │ └── summary.txt │ │ ├── sl_rarefaction_100_2_Treatment │ │ ├── confusion_matrix.txt │ │ ├── cv_probabilities.txt │ │ ├── feature_importance_scores.txt │ │ ├── mislabeling.txt │ │ └── summary.txt │ │ ├── sl_rarefaction_100_3_Treatment │ │ ├── confusion_matrix.txt │ │ ├── cv_probabilities.txt │ │ ├── feature_importance_scores.txt │ │ ├── mislabeling.txt │ │ └── summary.txt │ │ ├── sl_rarefaction_100_4_Treatment │ │ ├── confusion_matrix.txt │ │ ├── cv_probabilities.txt │ │ ├── feature_importance_scores.txt │ │ ├── mislabeling.txt │ │ └── summary.txt │ │ ├── sl_rarefaction_100_5_Treatment │ │ ├── confusion_matrix.txt │ │ ├── cv_probabilities.txt │ │ ├── feature_importance_scores.txt │ │ ├── mislabeling.txt │ │ └── summary.txt │ │ ├── sl_rarefaction_100_6_Treatment │ │ ├── confusion_matrix.txt │ │ ├── cv_probabilities.txt │ │ ├── feature_importance_scores.txt │ │ ├── mislabeling.txt │ │ └── summary.txt │ │ ├── sl_rarefaction_100_7_Treatment │ │ ├── confusion_matrix.txt │ │ ├── cv_probabilities.txt │ │ ├── feature_importance_scores.txt │ │ ├── mislabeling.txt │ │ └── summary.txt │ │ ├── sl_rarefaction_100_8_Treatment │ │ ├── confusion_matrix.txt │ │ ├── cv_probabilities.txt │ │ ├── feature_importance_scores.txt │ │ ├── mislabeling.txt │ │ └── summary.txt │ │ └── sl_rarefaction_100_9_Treatment │ │ ├── confusion_matrix.txt │ │ ├── cv_probabilities.txt │ │ ├── feature_importance_scores.txt │ │ ├── mislabeling.txt │ │ └── summary.txt ├── transform_coordinate_matrices │ ├── bray_curtis_pc.txt │ ├── euclidean_pc.txt │ ├── s1_pc.txt │ ├── s1_s2_map.txt │ ├── s1_s3_map.txt │ ├── s2_pc.txt │ ├── s3_pc.txt │ ├── unweighted_unifrac_pc.txt │ └── weighted_unifrac_pc.txt ├── tree_compare │ ├── bootstrapped_trees │ │ ├── bs1.tre │ │ ├── bs2.tre │ │ ├── bs3.tre │ │ └── bs4.tre │ └── input_master_tree.tre ├── trflp_file_to_otu_table │ └── trflp_in.txt ├── truncate_fasta_qual_files │ ├── .DS_Store │ ├── seqs.fna │ └── seqs.qual ├── truncate_reverse_primer │ ├── Mapping_File_Rev_Primer.txt │ └── seqs.fna ├── unweight_fasta │ └── input.fna ├── upgma_cluster │ ├── beta_div.txt │ └── beta_div_folder │ │ ├── beta_div_1.txt │ │ ├── beta_div_2.txt │ │ ├── beta_div_3.txt │ │ └── beta_div_4.txt └── validate_mapping_file │ ├── .DS_Store │ └── Fasting_Map.txt ├── scripts ├── add_alpha_to_mapping_file.py ├── add_qiime_labels.py ├── adjust_seq_orientation.py ├── align_seqs.py ├── alpha_diversity.py ├── alpha_rarefaction.py ├── ampliconnoise.py ├── assign_taxonomy.py ├── beta_diversity.py ├── beta_diversity_through_plots.py ├── beta_significance.py ├── blast_wrapper.py ├── categorized_dist_scatterplot.py ├── check_id_map.py ├── clean_raxml_parsimony_tree.py ├── cluster_quality.py ├── collapse_samples.py ├── collate_alpha.py ├── compare_alpha_diversity.py ├── compare_categories.py ├── compare_distance_matrices.py ├── compare_taxa_summaries.py ├── compare_trajectories.py ├── compute_core_microbiome.py ├── compute_taxonomy_ratios.py ├── conditional_uncovered_probability.py ├── consensus_tree.py ├── convert_fastaqual_fastq.py ├── convert_unifrac_sample_mapping_to_otu_table.py ├── core_diversity_analyses.py ├── count_seqs.py ├── demultiplex_fasta.py ├── denoise_wrapper.py ├── denoiser.py ├── denoiser_preprocess.py ├── denoiser_worker.py ├── detrend.py ├── differential_abundance.py ├── dissimilarity_mtx_stats.py ├── distance_matrix_from_mapping.py ├── estimate_observation_richness.py ├── exclude_seqs_by_blast.py ├── extract_barcodes.py ├── extract_reads_from_interleaved_file.py ├── extract_seqs_by_sample_id.py ├── 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 ├── group_significance.py ├── identify_chimeric_seqs.py ├── identify_missing_files.py ├── identify_paired_differences.py ├── inflate_denoiser_output.py ├── jackknifed_beta_diversity.py ├── join_paired_ends.py ├── load_remote_mapping_file.py ├── make_2d_plots.py ├── make_bipartite_network.py ├── make_bootstrapped_tree.py ├── make_distance_boxplots.py ├── make_distance_comparison_plots.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_rarefaction_plots.py ├── make_tep.py ├── map_reads_to_reference.py ├── merge_mapping_files.py ├── merge_otu_maps.py ├── merge_otu_tables.py ├── multiple_extract_barcodes.py ├── multiple_join_paired_ends.py ├── multiple_rarefactions.py ├── multiple_rarefactions_even_depth.py ├── multiple_split_libraries_fastq.py ├── neighbor_joining.py ├── nmds.py ├── normalize_table.py ├── observation_metadata_correlation.py ├── otu_category_significance.py ├── parallel_align_seqs_pynast.py ├── parallel_alpha_diversity.py ├── parallel_assign_taxonomy_blast.py ├── parallel_assign_taxonomy_rdp.py ├── parallel_assign_taxonomy_uclust.py ├── parallel_beta_diversity.py ├── parallel_blast.py ├── parallel_identify_chimeric_seqs.py ├── parallel_map_reads_to_reference.py ├── parallel_merge_otu_tables.py ├── parallel_multiple_rarefactions.py ├── parallel_pick_otus_blast.py ├── parallel_pick_otus_sortmerna.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_rep_set.py ├── plot_rank_abundance_graph.py ├── plot_semivariogram.py ├── plot_taxa_summary.py ├── poller.py ├── principal_coordinates.py ├── print_metadata_stats.py ├── print_qiime_config.py ├── process_iseq.py ├── process_qseq.py ├── process_sff.py ├── quality_scores_plot.py ├── relatedness.py ├── shared_phylotypes.py ├── simsam.py ├── single_rarefaction.py ├── sort_otu_table.py ├── split_libraries.py ├── split_libraries_fastq.py ├── split_libraries_lea_seq.py ├── split_otu_table.py ├── split_otu_table_by_taxonomy.py ├── split_sequence_file_on_sample_ids.py ├── start_parallel_jobs.py ├── start_parallel_jobs_sc.py ├── start_parallel_jobs_slurm.py ├── start_parallel_jobs_torque.py ├── subsample_fasta.py ├── summarize_otu_by_cat.py ├── summarize_taxa.py ├── summarize_taxa_through_plots.py ├── supervised_learning.py ├── 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 ├── unweight_fasta.py ├── upgma_cluster.py ├── validate_demultiplexed_fasta.py └── validate_mapping_file.py ├── setup.py └── tests ├── __init__.py ├── all_tests.py ├── test_add_alpha_to_mapping_file.py ├── test_add_qiime_labels.py ├── test_adjust_seq_orientation.py ├── test_align_seqs.py ├── test_alpha_diversity.py ├── test_assign_taxonomy.py ├── test_barcode.py ├── test_beta_diversity.py ├── test_beta_metrics.py ├── test_biplots.py ├── test_categorized_dist_scatterplot.py ├── test_clean_raxml_parsimony_tree.py ├── test_cluster_quality.py ├── test_collate_alpha.py ├── test_colors.py ├── test_compare_alpha_diversity.py ├── test_compare_categories.py ├── test_compare_distance_matrices.py ├── test_compare_taxa_summaries.py ├── test_compare_trajectories.py ├── test_compute_taxonomy_ratios.py ├── test_convert_fastaqual_fastq.py ├── test_core_microbiome.py ├── test_demultiplex_fasta.py ├── test_denoise_wrapper.py ├── test_denoiser ├── test_cluster_util.py ├── test_denoise_postprocess.py ├── test_denoiser.py ├── test_flowgram_clustering.py ├── test_flowgram_filter.py ├── test_make_cluster_jobs.py ├── test_preprocess.py ├── test_settings.py └── test_utils.py ├── test_detrend.py ├── test_differential_abundance.py ├── test_distance_matrix_from_mapping.py ├── test_estimate_observation_richness.py ├── test_exclude_seqs_by_blast.py ├── test_extract_barcodes.py ├── test_filter.py ├── test_filter_alignment.py ├── test_filter_otus_by_sample.py ├── test_format.py ├── test_golay.py ├── test_group.py ├── test_hamming.py ├── test_hierarchical_cluster.py ├── test_identify_chimeric_seqs.py ├── test_join_paired_ends.py ├── test_make_2d_plots.py ├── test_make_bipartite_network.py ├── test_make_bootstrapped_tree.py ├── test_make_distance_boxplots.py ├── test_make_fastq.py ├── test_make_library_id_lists.py ├── test_make_otu_heatmap.py ├── test_make_otu_network.py ├── test_make_otu_table.py ├── test_make_per_library_sff.py ├── test_make_phylogeny.py ├── test_make_rarefaction_plots.py ├── test_map_reads_to_reference.py ├── test_normalize_table.py ├── test_otu_significance.py ├── test_parallel ├── test_align_seqs.py ├── test_alpha_diversity.py ├── test_assign_taxonomy.py ├── test_beta_diversity.py ├── test_blast.py ├── test_identify_chimeric_seqs.py ├── test_map_reads_to_reference.py ├── test_merge_otus.py ├── test_multiple_rarefactions.py ├── test_pick_otus.py └── test_util.py ├── test_parse.py ├── test_pick_otus.py ├── test_pick_rep_set.py ├── test_plot_rank_abundance_graph.py ├── test_plot_semivariogram.py ├── test_plot_taxa_summary.py ├── test_principal_coordinates.py ├── test_process_sff.py ├── test_quality_scores_plot.py ├── test_rarefaction.py ├── test_relatedness.py ├── test_remote.py ├── test_shared_phylotypes.py ├── test_simsam.py ├── test_sort.py ├── test_split.py ├── test_split_libraries.py ├── test_split_libraries_fastq.py ├── test_split_libraries_lea_seq.py ├── test_stats.py ├── test_summarize_taxa.py ├── test_supervised_learning.py ├── test_support_files ├── F6AVWTA │ ├── F6AVWTA01.sff │ ├── F6AVWTA01 │ │ ├── B-2004-03-S1.sff │ │ ├── B-2004-04-S1.sff │ │ ├── B-2004-08-S1.sff │ │ ├── B-2005-06-S1.sff │ │ ├── B-2006-03-S1.sff │ │ └── bodysites_study_default_F6AVWTA01.sff │ ├── F6AVWTA02.sff │ └── F6AVWTA02 │ │ ├── B-2008-05-S1.sff │ │ ├── B-2008-08-S1.sff │ │ ├── B-2009-06-S1.sff │ │ ├── B-2011-01-S1.sff │ │ ├── B-2011-02-S1.sff │ │ └── bodysites_study_default_F6AVWTA02.sff ├── Fasting_Example.sff.txt ├── qiime_tutorial_split_lib_seqs_subset.fna ├── test.sff └── test_gz.sff.gz ├── test_transform_coordinate_matrices.py ├── test_tree_compare.py ├── test_trim_sff_primers.py ├── test_truncate_fasta_qual_files.py ├── test_truncate_reverse_primer.py ├── test_util.py ├── test_validate_demultiplexed_fasta.py ├── test_validate_mapping_file.py └── test_workflow ├── test_ampliconnoise.py ├── test_core_diversity_analyses.py ├── test_downstream.py ├── test_pick_open_reference_otus.py ├── test_preprocess.py ├── test_upstream.py └── test_util.py /.mailmap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/qiime/HEAD/.mailmap -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/qiime/HEAD/CONTRIBUTING.md -------------------------------------------------------------------------------- /COPYING.txt: 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