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- Committer: Package Import Robot
- Date: 2013-06-17 18:28:26 UTC
- mfrom: (9.1.2 sid)
- Revision ID: package-import@ubuntu.com-20130617182826-376az5ad080a0sfe
Upload preparations done for BioLinux to Debian
- files added:
- .pc/fix_path_for_support_files/qiime
- .pc/fix_typo_in_error_message
- .pc/fix_typo_in_error_message/scripts
- .pc/remove_matplotlib_warning
- .pc/remove_matplotlib_warning/scripts
- examples
- examples/ipynb
- examples/qiime_tutorial
- examples/qiime_tutorial/18S_tutorial_files
- qiime/workflow
- qiime_test_data
- qiime_test_data/add_alpha_to_mapping_file
- qiime_test_data/add_qiime_labels
- qiime_test_data/add_qiime_labels/combined_fasta
- qiime_test_data/add_qiime_labels/fasta_dir
- qiime_test_data/adjust_seq_orientation
- qiime_test_data/align_seqs
- qiime_test_data/align_seqs/infernal_aligned
- qiime_test_data/align_seqs/muscle_alignment
- qiime_test_data/align_seqs/pynast_aligned
- qiime_test_data/align_seqs/pynast_aligned_defaults
- qiime_test_data/alpha_diversity
- qiime_test_data/alpha_diversity/adiv_chao1_pd
- qiime_test_data/alpha_diversity/otu_tables
- qiime_test_data/alpha_rarefaction
- qiime_test_data/alpha_rarefaction/arare_max100
- qiime_test_data/alpha_rarefaction/arare_max100/alpha_div
- qiime_test_data/alpha_rarefaction/arare_max100/alpha_div_collated
- qiime_test_data/alpha_rarefaction/arare_max100/alpha_rarefaction_plots
- qiime_test_data/alpha_rarefaction/arare_max100/alpha_rarefaction_plots/average_plots
- qiime_test_data/alpha_rarefaction/arare_max100/alpha_rarefaction_plots/average_tables
- qiime_test_data/alpha_rarefaction/arare_max100/alpha_rarefaction_plots/html_plots
- qiime_test_data/alpha_rarefaction/arare_max100/rarefaction
- qiime_test_data/alpha_rarefaction/jobs
- qiime_test_data/ampliconnoise
- qiime_test_data/assign_taxonomy
- qiime_test_data/beta_diversity
- qiime_test_data/beta_diversity/beta_div
- qiime_test_data/beta_diversity/otu_tables
- qiime_test_data/beta_diversity_through_plots
- qiime_test_data/beta_diversity_through_plots/bdiv_even100
- qiime_test_data/beta_diversity_through_plots/bdiv_even100/unweighted_unifrac_2d_continuous
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- qiime_test_data/beta_diversity_through_plots/bdiv_even100/unweighted_unifrac_2d_continuous/20120314103522udFphID5lVnUkWQ0i7TW/20120314103522yTGdENkY0ch21hh0zhOy
- qiime_test_data/beta_diversity_through_plots/bdiv_even100/unweighted_unifrac_2d_continuous/js
- qiime_test_data/beta_diversity_through_plots/bdiv_even100/unweighted_unifrac_2d_discrete
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- qiime_test_data/beta_diversity_through_plots/bdiv_even100/unweighted_unifrac_2d_discrete/js
- qiime_test_data/beta_diversity_through_plots/bdiv_even100/unweighted_unifrac_3d_continuous
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- qiime_test_data/beta_significance
- qiime_test_data/blast_wrapper
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- qiime_test_data/cluster_quality
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- qiime_test_data/collate_alpha/collated_alpha
- qiime_test_data/compare_3d_plots
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- qiime_test_data/compare_3d_plots/jar
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- qiime_test_data/compare_3d_plots/test/jar
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- qiime_test_data/compare_distance_matrices
- qiime_test_data/compare_distance_matrices/mantel_correlogram_out
- qiime_test_data/compare_distance_matrices/mantel_out
- qiime_test_data/compare_distance_matrices/partial_mantel_out
- qiime_test_data/compare_taxa_summaries
- qiime_test_data/compare_taxa_summaries/taxa_comp
- qiime_test_data/compare_taxa_summaries/taxa_comp_detailed
- qiime_test_data/compare_taxa_summaries/taxa_comp_one_tailed
- qiime_test_data/compare_taxa_summaries/taxa_comp_using_sample_id_map
- qiime_test_data/compute_core_microbiome
- qiime_test_data/compute_core_microbiome/otu_table_core
- qiime_test_data/compute_core_microbiome/otu_table_core_fast
- qiime_test_data/conditional_uncovered_probability
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- qiime_test_data/convert_fastaqual_fastq
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- qiime_test_data/convert_otu_table_to_unifrac_sample_mapping
- qiime_test_data/convert_unifrac_sample_mapping_to_otu_table
- qiime_test_data/core_diversity_analyses
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- qiime_test_data/core_diversity_analyses/core_output/arare_max20/alpha_div
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- qiime_test_data/core_diversity_analyses/core_output/arare_max20/alpha_div_collated/PD_whole_tree.txt
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- qiime_test_data/core_diversity_analyses/core_output/taxa_plots/taxa_summary_plots/js
- qiime_test_data/core_diversity_analyses/core_output/taxa_plots/taxa_summary_plots/raw_data
- qiime_test_data/core_diversity_analyses/core_output/taxa_plots_SampleType
- qiime_test_data/core_diversity_analyses/core_output/taxa_plots_SampleType/taxa_summary_plots
- qiime_test_data/core_diversity_analyses/core_output/taxa_plots_SampleType/taxa_summary_plots/charts
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- qiime_test_data/core_diversity_analyses/core_output/taxa_plots_day
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- qiime_test_data/core_diversity_analyses/core_output/taxa_plots_day/taxa_summary_plots/raw_data
- qiime_test_data/count_seqs
- qiime_test_data/demultiplex_fasta
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- qiime_test_data/dissimilarity_mtx_stats
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- qiime_test_data/dissimilarity_mtx_stats/dists
- qiime_test_data/distance_matrix_from_mapping
- qiime_test_data/exclude_seqs_by_blast
- qiime_test_data/exclude_seqs_by_blast/exclude_seqs
- qiime_test_data/extract_seqs_by_sample_id
- qiime_test_data/filter_alignment
- qiime_test_data/filter_alignment/filtered_alignment
- qiime_test_data/filter_alignment/filtered_alignment_gap_95
- qiime_test_data/filter_distance_matrix
- qiime_test_data/filter_fasta
- qiime_test_data/filter_otus_by_sample
- qiime_test_data/filter_otus_by_sample/filtered_otus
- qiime_test_data/filter_otus_from_otu_table
- qiime_test_data/filter_samples_from_otu_table
- qiime_test_data/filter_taxa_from_otu_table
- qiime_test_data/filter_tree
- qiime_test_data/fix_arb_fasta
- qiime_test_data/identify_chimeric_seqs
- qiime_test_data/identify_chimeric_seqs/usearch61_chimera_checking
- qiime_test_data/identify_missing_files
- qiime_test_data/identify_missing_files/ALIGN_BQ7_
- qiime_test_data/inflate_denoiser_output
- qiime_test_data/inflate_denoiser_output/combined
- qiime_test_data/inflate_denoiser_output/combined/denoised_1st_half
- qiime_test_data/inflate_denoiser_output/combined/denoised_2nd_half
- qiime_test_data/inflate_denoiser_output/combined/split_libraries_output_1st_half
- qiime_test_data/inflate_denoiser_output/combined/split_libraries_output_2nd_half
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- qiime_test_data/parallel_blast/jobs
- qiime_test_data/parallel_identify_chimeric_seqs
- qiime_test_data/parallel_map_reads_to_reference
- qiime_test_data/parallel_map_reads_to_reference/blat_mapped
- qiime_test_data/parallel_map_reads_to_reference/bwa-short_mapped
- qiime_test_data/parallel_map_reads_to_reference/usearch_mapped
- qiime_test_data/parallel_multiple_rarefactions
- qiime_test_data/parallel_multiple_rarefactions/even_otu_tables
- qiime_test_data/parallel_multiple_rarefactions/jobs
- qiime_test_data/parallel_multiple_rarefactions/rarefied_otu_tables
- qiime_test_data/parallel_pick_otus_blast
- qiime_test_data/parallel_pick_otus_blast/blast_otus
- qiime_test_data/parallel_pick_otus_trie
- qiime_test_data/parallel_pick_otus_trie/trie_otus
- qiime_test_data/parallel_pick_otus_uclust_ref
- qiime_test_data/parallel_pick_otus_uclust_ref/ucref_otus
- qiime_test_data/parallel_pick_otus_usearch61_ref
- qiime_test_data/parallel_pick_otus_usearch61_ref/usearch_ref_otus
- qiime_test_data/pick_closed_reference_otus
- qiime_test_data/pick_closed_reference_otus/otus
- qiime_test_data/pick_closed_reference_otus/otus/uclust_ref_picked_otus
- qiime_test_data/pick_closed_reference_otus/otus_usearch
- qiime_test_data/pick_closed_reference_otus/otus_usearch/usearch_ref_picked_otus
- qiime_test_data/pick_closed_reference_otus/otus_w_tax
- qiime_test_data/pick_closed_reference_otus/otus_w_tax/uclust_ref_picked_otus
- qiime_test_data/pick_de_novo_otus
- qiime_test_data/pick_de_novo_otus/otus
- qiime_test_data/pick_de_novo_otus/otus/pynast_aligned_seqs
- qiime_test_data/pick_de_novo_otus/otus/rdp_assigned_taxonomy
- qiime_test_data/pick_de_novo_otus/otus/rep_set
- qiime_test_data/pick_de_novo_otus/otus/uclust_picked_otus
- qiime_test_data/pick_open_reference_otus
- qiime_test_data/pick_open_reference_otus/ucrss
- qiime_test_data/pick_open_reference_otus/ucrss/prefilter_otus
- qiime_test_data/pick_open_reference_otus/ucrss/pynast_aligned_seqs
- qiime_test_data/pick_open_reference_otus/ucrss/rdp_assigned_taxonomy
- qiime_test_data/pick_open_reference_otus/ucrss/step1_otus
- qiime_test_data/pick_open_reference_otus/ucrss/step2_otus
- qiime_test_data/pick_open_reference_otus/ucrss/step3_otus
- qiime_test_data/pick_open_reference_otus/ucrss/step4_otus
- qiime_test_data/pick_open_reference_otus/ucrss_iter
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- qiime_test_data/pick_open_reference_otus/ucrss_iter/0/prefilter_otus
- qiime_test_data/pick_open_reference_otus/ucrss_iter/0/step1_otus
- qiime_test_data/pick_open_reference_otus/ucrss_iter/0/step2_otus
- qiime_test_data/pick_open_reference_otus/ucrss_iter/0/step3_otus
- qiime_test_data/pick_open_reference_otus/ucrss_iter/0/step4_otus
- qiime_test_data/pick_open_reference_otus/ucrss_iter/1
- qiime_test_data/pick_open_reference_otus/ucrss_iter/1/prefilter_otus
- qiime_test_data/pick_open_reference_otus/ucrss_iter/1/step1_otus
- qiime_test_data/pick_open_reference_otus/ucrss_iter/1/step2_otus
- qiime_test_data/pick_open_reference_otus/ucrss_iter/1/step3_otus
- qiime_test_data/pick_open_reference_otus/ucrss_iter/1/step4_otus
- qiime_test_data/pick_open_reference_otus/ucrss_iter/pynast_aligned_seqs
- qiime_test_data/pick_open_reference_otus/ucrss_iter/rdp_assigned_taxonomy
- qiime_test_data/pick_open_reference_otus/ucrss_iter_no_tax
- qiime_test_data/pick_open_reference_otus/ucrss_iter_no_tax/0
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- qiime_test_data/pick_open_reference_otus/ucrss_iter_no_tax/1/step2_otus/subsampled_failures_otus.log
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- qiime_test_data/pick_open_reference_otus/ucrss_iter_no_tax/pynast_aligned_seqs
- qiime_test_data/pick_open_reference_otus/ucrss_iter_no_tax/pynast_aligned_seqs/rep_set_aligned.fasta
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- qiime_test_data/pick_open_reference_otus/ucrss_iter_no_tree/0/step2_otus
- qiime_test_data/pick_open_reference_otus/ucrss_iter_no_tree/0/step3_otus
- qiime_test_data/pick_open_reference_otus/ucrss_iter_no_tree/0/step4_otus
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- qiime_test_data/pick_open_reference_otus/ucrss_iter_no_tree/1/step4_otus
- qiime_test_data/pick_open_reference_otus/ucrss_iter_no_tree/rdp_assigned_taxonomy
- qiime_test_data/pick_open_reference_otus/ucrss_usearch
- qiime_test_data/pick_open_reference_otus/ucrss_usearch/prefilter_otus
- qiime_test_data/pick_open_reference_otus/ucrss_usearch/pynast_aligned_seqs
- qiime_test_data/pick_open_reference_otus/ucrss_usearch/rdp_assigned_taxonomy
- qiime_test_data/pick_open_reference_otus/ucrss_usearch/step1_otus
- qiime_test_data/pick_open_reference_otus/ucrss_usearch/step2_otus
- qiime_test_data/pick_open_reference_otus/ucrss_usearch/step3_otus
- qiime_test_data/pick_open_reference_otus/ucrss_usearch/step4_otus
- qiime_test_data/pick_otus
- qiime_test_data/pick_otus/blast_picked_otus
- qiime_test_data/pick_otus/blast_picked_otus_90_percent
- qiime_test_data/pick_otus/blast_picked_otus_prebuilt_db
- qiime_test_data/pick_otus/cdhit_picked_otus
- qiime_test_data/pick_otus/cdhit_picked_otus_filter
- qiime_test_data/pick_otus/cdhit_picked_otus_trie_prefilter
- qiime_test_data/pick_otus/mothur_picked_otus
- qiime_test_data/pick_otus/mothur_picked_otus_90_percent
- qiime_test_data/pick_otus/mothur_picked_otus_nn
- qiime_test_data/pick_otus/picked_otus_90_percent_rev
- qiime_test_data/pick_otus/picked_otus_default
- qiime_test_data/pick_otus/prefix_suffix_picked_otus
- qiime_test_data/pick_otus/uclust_ref_picked_otus
- qiime_test_data/pick_otus/usearch_qf_results
- qiime_test_data/pick_otus/usearch_qf_results_no_ref_chim_detection
- qiime_test_data/pick_otus/usearch_qf_results_no_ref_chim_detection/usearch_cluster_err_corrected.log
- qiime_test_data/pick_rep_set
- qiime_test_data/plot_rank_abundance_graph
- qiime_test_data/plot_semivariogram
- qiime_test_data/plot_taxa_summary
- qiime_test_data/plot_taxa_summary/class_pie_n10_charts
- qiime_test_data/plot_taxa_summary/class_pie_n10_charts/charts
- qiime_test_data/plot_taxa_summary/class_pie_n10_charts/css
- qiime_test_data/plot_taxa_summary/class_pie_n10_charts/js
- qiime_test_data/plot_taxa_summary/class_pie_n10_charts/raw_data
- qiime_test_data/plot_taxa_summary/phylum_charts
- qiime_test_data/plot_taxa_summary/phylum_charts/charts
- qiime_test_data/plot_taxa_summary/phylum_charts/css
- qiime_test_data/plot_taxa_summary/phylum_charts/js
- qiime_test_data/plot_taxa_summary/phylum_charts/raw_data
- qiime_test_data/plot_taxa_summary/phylum_class_genus_charts
- qiime_test_data/plot_taxa_summary/phylum_class_genus_charts/charts
- qiime_test_data/plot_taxa_summary/phylum_class_genus_charts/css
- qiime_test_data/plot_taxa_summary/phylum_class_genus_charts/js
- qiime_test_data/plot_taxa_summary/phylum_class_genus_charts/raw_data
- qiime_test_data/plot_taxa_summary/sample_charts
- qiime_test_data/plot_taxa_summary/sample_charts/charts
- qiime_test_data/plot_taxa_summary/sample_charts/css
- qiime_test_data/plot_taxa_summary/sample_charts/js
- qiime_test_data/plot_taxa_summary/sample_charts/raw_data
- qiime_test_data/poller
- qiime_test_data/principal_coordinates
- qiime_test_data/principal_coordinates/beta_div_weighted_pcoa_results
- qiime_test_data/principal_coordinates/beta_div_weighted_unifrac
- qiime_test_data/print_metadata_stats
- qiime_test_data/quality_scores_plot
- qiime_test_data/quality_scores_plot/quality_histograms
- qiime_test_data/relatedness
- qiime_test_data/shared_phylotypes
- qiime_test_data/shared_phylotypes/rarefied_otu_tables
- qiime_test_data/shared_phylotypes/shared_otus
- qiime_test_data/simsam
- qiime_test_data/simsam/simsam_out1
- qiime_test_data/simsam/simsam_out2
- qiime_test_data/single_rarefaction
- qiime_test_data/sort_otu_table
- qiime_test_data/split_fasta_on_sample_ids
- qiime_test_data/split_fasta_on_sample_ids/out
- qiime_test_data/split_libraries
- qiime_test_data/split_libraries/Split_Library_Output
- qiime_test_data/split_libraries/Split_Library_Output_comma_separated
- qiime_test_data/split_libraries/Split_Library_Run1_Output
- qiime_test_data/split_libraries/Split_Library_Run2_Output
- qiime_test_data/split_libraries/split_Library_output_8bp
- qiime_test_data/split_libraries/split_libraries_output_revprimer
- qiime_test_data/split_libraries_fastq
- qiime_test_data/split_libraries_fastq/slout_q20
- qiime_test_data/split_libraries_fastq/slout_single_sample_q20
- qiime_test_data/split_otu_table
- qiime_test_data/split_otu_table/per_study_otu_tables
- qiime_test_data/split_otu_table_by_taxonomy
- qiime_test_data/split_otu_table_by_taxonomy/L3
- qiime_test_data/start_parallel_jobs
- qiime_test_data/start_parallel_jobs_sc
- qiime_test_data/start_parallel_jobs_torque
- qiime_test_data/subsample_fasta
- qiime_test_data/summarize_otu_by_cat
- qiime_test_data/summarize_taxa
- qiime_test_data/summarize_taxa/tax
- qiime_test_data/summarize_taxa/tax_mapping
- qiime_test_data/summarize_taxa_through_plots
- qiime_test_data/summarize_taxa_through_plots/taxa_summary
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- qiime_test_data/summarize_taxa_through_plots/taxa_summary/taxa_summary_plots/charts
- qiime_test_data/summarize_taxa_through_plots/taxa_summary/taxa_summary_plots/css
- qiime_test_data/summarize_taxa_through_plots/taxa_summary/taxa_summary_plots/js
- qiime_test_data/summarize_taxa_through_plots/taxa_summary/taxa_summary_plots/raw_data
- qiime_test_data/summarize_taxa_through_plots/taxa_summary_by_treatment
- qiime_test_data/summarize_taxa_through_plots/taxa_summary_by_treatment/taxa_summary_plots
- qiime_test_data/summarize_taxa_through_plots/taxa_summary_by_treatment/taxa_summary_plots/charts
- qiime_test_data/summarize_taxa_through_plots/taxa_summary_by_treatment/taxa_summary_plots/css
- qiime_test_data/summarize_taxa_through_plots/taxa_summary_by_treatment/taxa_summary_plots/js
- qiime_test_data/summarize_taxa_through_plots/taxa_summary_by_treatment/taxa_summary_plots/raw_data
- qiime_test_data/supervised_learning
- qiime_test_data/supervised_learning/ml
- qiime_test_data/supervised_learning/ml_cv10
- qiime_test_data/supervised_learning/ml_ntree1000
- qiime_test_data/supervised_learning/rarefied_tables
- qiime_test_data/supervised_learning/sl_rarefied_tables_cv10
- qiime_test_data/supervised_learning/sl_rarefied_tables_cv10/sl_rarefaction_100_0_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_cv10/sl_rarefaction_100_1_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_cv10/sl_rarefaction_100_2_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_cv10/sl_rarefaction_100_3_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_cv10/sl_rarefaction_100_4_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_cv10/sl_rarefaction_100_5_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_cv10/sl_rarefaction_100_6_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_cv10/sl_rarefaction_100_7_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_cv10/sl_rarefaction_100_8_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_cv10/sl_rarefaction_100_9_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_oob
- qiime_test_data/supervised_learning/sl_rarefied_tables_oob/sl_rarefaction_100_0_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_oob/sl_rarefaction_100_1_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_oob/sl_rarefaction_100_2_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_oob/sl_rarefaction_100_3_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_oob/sl_rarefaction_100_4_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_oob/sl_rarefaction_100_5_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_oob/sl_rarefaction_100_6_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_oob/sl_rarefaction_100_7_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_oob/sl_rarefaction_100_8_Treatment
- qiime_test_data/supervised_learning/sl_rarefied_tables_oob/sl_rarefaction_100_9_Treatment
- qiime_test_data/transform_coordinate_matrices
- qiime_test_data/transform_coordinate_matrices/mc_procrustes_output
- qiime_test_data/transform_coordinate_matrices/procrustes_output
- qiime_test_data/tree_compare
- qiime_test_data/tree_compare/bootstrapped_trees
- qiime_test_data/tree_compare/output
- qiime_test_data/trflp_file_to_otu_table
- qiime_test_data/truncate_fasta_qual_files
- qiime_test_data/truncate_fasta_qual_files/filtered_seqs
- qiime_test_data/truncate_reverse_primer
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- qiime_test_data/unweight_fasta
- qiime_test_data/upgma_cluster
- qiime_test_data/upgma_cluster/beta_div_folder
- qiime_test_data/upgma_cluster/beta_div_folder_results
- tests/test_workflow
- files removed:
- .pc/fix_path_for_support_files/scripts
- .pc/fix_t_test_bug
- .pc/fix_t_test_bug/qiime
- .pc/fix_t_test_bug/scripts
- .pc/fix_t_test_bug/tests
- doc/_build
- qiime/support_files/denoiser/bin
- qiime/support_files/html_templates
- qiime_tutorial
- qiime_tutorial/18S_tutorial_files
- web
- web/home_static
- web/home_static/images
- web/home_static/nih-cloud-apr2012
- web/home_static/nih-cloud-apr2012/NIHCloudDemo_Complete_files
- web/home_static/nih-cloud-apr2012/NIHCloudDemo_Fast_files
- web/home_static/nih-cloud-apr2012/Timing_files
- web/home_static/nih-cloud-apr2012/VariableRegionPositionBoundaries_files
- files modified:
- .pc/applied-patches
added
removed
qiime_test_data/core_diversity_analyses/core_output/arare_max20/alpha_rarefaction_plots/average_tables/chao1SampleID.txt
