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doc/images/create_an_ebs_volume.png
doc/images/cyberduck_create_output_file.png
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doc/images/shotgun_analysis_gn_ec_summary.png
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doc/images/shotgun_analysis_gn_pcoa.png
doc/images/sink_predictions_pie_NICU_BabyBedside.png
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doc/install/index.rst
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doc/install/qiime_config.rst
doc/install/upgrade.rst
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doc/scripts/add_qiime_labels.rst
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doc/scripts/ampliconnoise.rst
doc/scripts/assign_taxonomy.rst
doc/scripts/beta_diversity.rst
doc/scripts/beta_diversity_through_plots.rst
doc/scripts/beta_significance.rst
doc/scripts/blast_wrapper.rst
doc/scripts/categorized_dist_scatterplot.rst
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doc/scripts/subsample_fasta.rst
doc/scripts/summarize_taxa.rst
doc/scripts/summarize_taxa_through_plots.rst
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doc/tutorials/denoising_454_data.rst
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doc/tutorials/processing_illumina_data.rst
doc/tutorials/procrustes_analysis.rst
doc/tutorials/remote_mapping_files.rst
doc/tutorials/retraining_rdp.rst
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doc/tutorials/unix_commands.rst
doc/tutorials/usearch_quality_filter.rst
doc/tutorials/working_with_aws.rst
doc/tutorials/working_with_biom_tables.rst
examples/ipynb/Fungal-ITS-analysis.ipynb
examples/ipynb/illumina_overview_tutorial.ipynb
examples/ipynb/illumina_overview_tutorial_workshop_template.ipynb
qiime/__init__.py
qiime/add_alpha_to_mapping_file.py
qiime/add_qiime_labels.py
qiime/adjust_seq_orientation.py
qiime/align_seqs.py
qiime/alpha_diversity.py
qiime/assign_taxonomy.py
qiime/barcode.py
qiime/beta_diversity.py
qiime/beta_metrics.py
qiime/biplots.py
qiime/categorized_dist_scatterplot.py
qiime/check_id_map.py
qiime/clean_raxml_parsimony_tree.py
qiime/cluster_quality.py
qiime/collate_alpha.py
qiime/colors.py
qiime/compare_alpha_diversity.py
qiime/compare_categories.py
qiime/compare_distance_matrices.py
qiime/compare_taxa_summaries.py
qiime/compare_trajectories.py
qiime/compute_taxonomy_ratios.py
qiime/convert_fastaqual_fastq.py
qiime/core_microbiome.py
qiime/demultiplex_fasta.py
qiime/denoise_wrapper.py
qiime/detrend.py
qiime/differential_abundance.py
qiime/distance_matrix_from_mapping.py
qiime/estimate_observation_richness.py
qiime/exclude_seqs_by_blast.py
qiime/extract_barcodes.py
qiime/filter.py
qiime/filter_alignment.py
qiime/filter_otus_by_sample.py
qiime/format.py
qiime/golay.py
qiime/group.py
qiime/hamming.py
qiime/hierarchical_cluster.py
qiime/identify_chimeric_seqs.py
qiime/join_paired_ends.py
qiime/make_2d_plots.py
qiime/make_bipartite_network.py
qiime/make_bootstrapped_tree.py
qiime/make_distance_boxplots.py
qiime/make_fastq.py
qiime/make_library_id_lists.py
qiime/make_otu_heatmap.py
qiime/make_otu_network.py
qiime/make_otu_table.py
qiime/make_per_library_sff.py
qiime/make_phylogeny.py
qiime/make_rarefaction_plots.py
qiime/map_reads_to_reference.py
qiime/nmds.py
qiime/normalize_table.py
qiime/otu_significance.py
qiime/parse.py
qiime/pick_otus.py
qiime/pick_rep_set.py
qiime/plot_rank_abundance_graph.py
qiime/plot_semivariogram.py
qiime/plot_taxa_summary.py
qiime/principal_coordinates.py
qiime/process_sff.py
qiime/quality_scores_plot.py
qiime/rarefaction.py
qiime/relatedness_library.py
qiime/remote.py
qiime/shared_phylotypes.py
qiime/simsam.py
qiime/sort.py
qiime/split.py
qiime/split_libraries.py
qiime/split_libraries_fastq.py
qiime/split_libraries_lea_seq.py
qiime/stats.py
qiime/summarize_taxa.py
qiime/supervised_learning.py
qiime/test.py
qiime/transform_coordinate_matrices.py
qiime/tree_compare.py
qiime/trim_sff_primers.py
qiime/truncate_fasta_qual_files.py
qiime/truncate_reverse_primer.py
qiime/util.py
qiime/validate_demultiplexed_fasta.py
qiime.egg-info/PKG-INFO
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qiime/parallel/identify_chimeric_seqs.py
qiime/parallel/map_reads_to_reference.py
qiime/parallel/merge_otus.py
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qiime/support_files/denoiser/FlowgramAlignment/FlowgramUtils.lhs
qiime/support_files/denoiser/FlowgramAlignment/Makefile
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qiime/support_files/denoiser/TestData/test_flow_file.dat
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qiime/workflow/__init__.py
qiime/workflow/ampliconnoise.py
qiime/workflow/core_diversity_analyses.py
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qiime_test_data/alpha_diversity/otu_tables/otu_table_3.biom
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qiime_test_data/alpha_rarefaction/otu_table.biom
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qiime_test_data/ampliconnoise/Fasting_Example.sff.txt
qiime_test_data/ampliconnoise/Fasting_Map.txt
qiime_test_data/assign_taxonomy/id_to_taxonomy.txt
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qiime_test_data/assign_taxonomy/mothur_ref_seq_set.fna
qiime_test_data/assign_taxonomy/mothur_repr_set_seqs.fasta
qiime_test_data/assign_taxonomy/read_1.seqs.fna
qiime_test_data/assign_taxonomy/read_2.seqs.fna
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qiime_test_data/assign_taxonomy/repr_set_seqs.fasta
qiime_test_data/assign_taxonomy/rtax_id_to_taxonomy.txt
qiime_test_data/assign_taxonomy/rtax_ref_seq_set.fna
qiime_test_data/assign_taxonomy/rtax_repr_set_seqs.fasta
qiime_test_data/assign_taxonomy/uclust_assigned_taxonomy/repr_set_seqs_tax_assignments.log
qiime_test_data/assign_taxonomy/uclust_assigned_taxonomy/repr_set_seqs_tax_assignments.txt
qiime_test_data/beta_diversity/otu_table.biom
qiime_test_data/beta_diversity/rep_set.tre
qiime_test_data/beta_diversity/otu_tables/otu_table_1.biom
qiime_test_data/beta_diversity/otu_tables/otu_table_2.biom
qiime_test_data/beta_diversity/otu_tables/otu_table_3.biom
qiime_test_data/beta_diversity_through_plots/Fasting_Map.txt
qiime_test_data/beta_diversity_through_plots/otu_table.biom
qiime_test_data/beta_diversity_through_plots/rep_set.tre
qiime_test_data/beta_significance/otu_table.biom
qiime_test_data/beta_significance/rep_set.tre
qiime_test_data/blast_wrapper/inseqs.fasta
qiime_test_data/blast_wrapper/refseqs.fasta
qiime_test_data/cluster_quality/Fasting_Map.txt
qiime_test_data/cluster_quality/quality_dob.txt
qiime_test_data/cluster_quality/quality_treatment.txt
qiime_test_data/cluster_quality/weighted_unifrac_otu_table.txt
qiime_test_data/collapse_samples/map.txt
qiime_test_data/collapse_samples/table.biom
qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_101_1.txt
qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_101_3.txt
qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_101_7.txt
qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_101_9.txt
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qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_114_3.txt
qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_114_7.txt
qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_114_9.txt
qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_127_1.txt
qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_127_3.txt
qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_127_7.txt
qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_127_9.txt
qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_140_1.txt
qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_140_3.txt
qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_140_7.txt
qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_140_9.txt
qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_23_1.txt
qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_23_3.txt
qiime_test_data/collate_alpha/alpha_div/alpha_rarefaction_23_7.txt
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