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Index

A | B | C | D | E | F | G | I | J | L | M | N | P | Q | R | S | T | U | V

A

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

B

beta_diversity.py
beta_diversity_through_plots.py
beta_significance.py
blast_wrapper.py

C

categorized_dist_scatterplot.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
core_diversity_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

estimate_observation_richness.py
exclude_seqs_by_blast.py
extract_barcodes.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

G

group_significance.py

I

identify_chimeric_seqs.py
identify_missing_files.py
identify_paired_differences.py
inflate_denoiser_output.py
insert_seqs_into_tree.py
Installing QIIME

J

jackknifed_beta_diversity.py
join_paired_ends.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_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

P

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_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
poller_example.py
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
validate_mapping_file.py

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