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A | B | C | D | E | F | I | J | M | N | O | P | Q | S | T | U

A

add_taxa.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_3d_plots.py
beta_diversity_through_plots.py
beta_significance.py
blast_wrapper.py

C

categorized_dist_scatterplot.py
check_id_map.py
cluster_quality.py
collate_alpha.py
compare_3d_plots.py
compare_alpha_diversity.py
compare_distance_matrices.py
consensus_tree.py
convert_otu_table_to_unifrac_sample_mapping.py
convert_unifrac_sample_mapping_to_otu_table.py
core_qiime_analyses.py
cytoscape

D

denoise.py
denoise_wrapper.py
denoiser.py
denoiser_postprocess.py
denoiser_preprocess.py
denoiser_worker.py
dissimilarity_mtx_stats.py
Documentation

E

exclude_seqs_by_blast.py
extract_seqs_by_sample_id.py

F

filter_alignment.py
filter_by_metadata.py
filter_fasta.py
filter_otu_table.py
filter_otus_by_sample.py
filter_tree.py
fix_arb_fasta.py

I

identify_chimeric_seqs.py
identify_missing_files.py
inflate_denoiser_output.py
Installing QIIME

J

jackknifed_beta_diversity.py

M

make_2d_plots.py
make_3d_plots.py
make_bootstrapped_tree.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_pie_charts.py
make_prefs_file.py
make_qiime_py_file.py
make_qiime_rst_file.py
make_rarefaction_plots.py
make_tep.py
merge_denoiser_output.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_multiple_rarefactions.py
parallel_pick_otus_blast.py
parallel_pick_otus_uclust_ref.py
per_library_stats.py
pick_otus.py
pick_otus_through_otu_table.py
pick_reference_otus_through_otu_table.py
pick_rep_set.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_qiime_config.py
process_iseq.py
process_qseq.py
process_sff.py

Q

quality_scores_plot.py

S

shared_phylotypes.py
simsam.py
single_rarefaction.py
sort_denoiser_output.py
sort_otu_table.py
split_libraries.py
split_libraries_fastq.py
split_libraries_illumina.py
split_otu_table.py
split_otu_table_by_taxonomy.py
start_parallel_jobs.py
start_parallel_jobs_torque.py
submit_to_mgrast.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

U

unweight_fasta.py
upgma_cluster.py

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