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searchindex.js
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searchindex.js
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Search.setIndex({envversion:42,terms:{line_color:35,aln:[140,137],entropi:[39,44],orthogon:189,"_log":1,unidentifi:39,yellow:[189,32,74,26],confidence_level:142,four:[64,102,177,178,179,121,159,146,147,148,136,189],secondli:178,prefix:[132,64,1,74,3],sleep:[66,140,133,120,51,83,106,109,187,173,135,30,14,61],seconds_to_sleep:[0,66,140,120,51,83,106,109,187,173,135,30,14,61],fig1:40,dist:[97,188],de_novo_chimera_detect:[18,121],consider:[189,133,177],whose:[126,196,44,38,186,190],specificcalcul:37,lgpl:98,jobs_to_start:[0,66,156,70,122,14,165,82,172,120,170,28,173,89,83,30,179,94,109,187,135,12,140,51,106,61],spacedefault:116,aug:18,tail_typ:[142,147,152,34],dist_unweighted_unifrac_full_tre:16,not_barcod:74,abundance_skew:[18,121],collated_alpha:[95,132,54],deviat:95,weighted_normalized_unifrac:65,under:[64,81,198,179,133,45,95,20,74,186,98,176,148,125],preprocess:[96,133,3],slowest:133,worth:133,creating_distance_comparison_plot:[152,34],lack:[5,195],everi:[64,2,44,53,116,15,198,20,21,26,31,130,133,36,136,189,197,192,146,54,201,152],quantil:132,downstream:[64,81,178,127,121,133,148,107,39,3,151,88,175,103],gg_otus_4feb2011:[142,5,146,36,198,136,115,143],pick_de_novo_otu:[82,178,158,174,138,62],tcttgtattaatcttcctttcagaaggctgtccaagagtagacggcaggttggatacgtgttactcacccgg:18,dist_euclidean:16,hardwar:9,sl_rarefied_tables_cv10:87,s_8_map:115,upstream:176,appar:195,install_script:98,lefthand:131,node_instance_typ:198,f__veillonellacea:103,aaaaaaaa:115,poolednonfast:200,make_bipartite_network:158,prefix_picked_otu:129,xyz:177,sorted_sample_ids_fp:114,unsubsambl:28,"607_1118":129,vector:37,technolog:[64,133,7,148,75,9],pd_whole_tree_alpha:132,mcintosh_:25,qual_score_window:148,filtered_align:44,merge_otu_t:158,g__serratia:136,speci:[16,172,81,37,121,133,39,136,189,103],miller:[121,159],naiv:5,variable_size_distance_class:147,seper:64,direct:[189,98,148,26],sturg:[147,31],horn:16,outputpath:102,consequ:98,second:[64,0,66,187,5,129,7,195,115,154,14,192,135,120,121,83,171,173,30,31,178,130,132,133,36,95,109,136,189,42,191,140,50,51,134,146,106,147,142,148,58,61],mc_procrustes_output:139,friendlyq:125,chen:37,even:[70,159,7,149,76,82,172,120,170,87,90,130,133,38,97,137,189,61,196,148,103,174],supervis:[98,158],parallel_multiple_rarefact:158,"454reads_1":3,ttgggccgtgtctcagtcccaatgtggccgtccgccctctc:189,fisher_alpha:25,accgcagagtca:[189,178,38,131],neg:[111,31,142,169,29,146,11,20,59,167],samples_to_keep:11,conduct:65,"new":[27,176,76],symmetr:[153,169,182,147,34,152],ever:[198,103],happi:115,metadata:[93,191],deflin:107,ongo:39,pick_closed_reference_otu:[158,174],subtre:108,jre1:98,"27f":74,displai:[37,35,195,123,59,55,38,74,21,58,189],no_single_ok_gener:5,accagacgatgctacgtagggggcaagcgttgtccggatttattgggcgtaaagcgcgtgtaggcggccaggtaggtccgttgtgaaaactggaggcttaac:115,never:[46,198,148,20],ellipisoid:[37,194],here:[66,2,156,5,6,70,159,7,122,189,74,138,187,117,14,165,135,81,82,172,198,123,121,83,18,20,176,173,88,24,143,180,26,89,90,69,30,31,178,179,130,169,133,36,94,115,38,39,97,136,9,12,98,45,47,175,113,103,51,146,106,55,200,120,109,61,186],src_fasttre:98,met:115,added_demultiplex_field:[64,148,74],accur:[90,98,145,36],parameter_fp:[82,172,156,170,70,122,160,28,94,75,12,165,89],path:76,interpret:[189,180,31],forens:97,forum:[81,49,84,115,76,9],margalef:25,correlogram:147,src_uclust:98,adopt:178,precis:[145,36],master_pcoa:[37,194],cogent:79,trie_reverse_seq:121,sjn:115,expected_out_fp:155,lanemask:[0,165,44,94,39,189,138,98,127],permit:1,denovootu34054:103,studi:[64,2,7,189,149,117,168,20,131,175,26,90,31,178,130,133,182,97,115,191,195,146,148,107,103],jackknife_sampl:43,portabl:9,seqs1:[133,122,10,12,103,62],seqs2:[133,122,10,12,103,62],usage_str:93,julia:81,look_ahead:145,brought:49,bashrc:98,unix:84,verbose_process_run_results_f:192,expected_out_fil:[179,155],moran:169,org:[1,156,5,70,160,28,162,10,74,75,165,190,177,82,172,198,169,170,121,122,34,87,176,89,31,178,94,12,98,191,142,147,201,152],"60_sorted_and_fil":146,txt:[1,2,3,4,5,29,7,8,10,11,13,15,17,125,21,22,23,26,30,31,34,35,36,38,39,40,41,12,43,114,48,50,51,52,53,54,56,57,58,59,103,174,63,64,65,70,149,74,75,77,82,86,87,88,89,90,95,96,97,98,100,61,104,62,44,108,109,110,112,113,28,116,172,120,121,122,124,20,37,127,128,129,130,131,132,133,134,136,138,139,32,142,145,146,147,148,151,152,153,154,155,156,157,126,159,160,161,162,185,167,168,169,170,171,173,175,177,178,179,180,182,183,184,186,187,115,190,192,194,195,196,197,199,200,201,202],f__sinobacteracea:103,unit:[81,2,177,121,150,39,34,138,9,192,152],highli:[178,47,98,81],extrapol:145,plot:[98,172],dna:[189,178,74],describ:[100,0,31,92,178,126,121,129,84,190,169,148,11,176,22,88,127,98,177],would:[153,64,187,37,70,159,7,44,41,10,74,196,117,177,81,121,18,171,20,21,22,88,24,180,26,90,128,31,178,179,33,133,36,194,95,38,186,136,189,138,98,175,102,142,152,182,32,146,148,107,201,58,59,61,174,115],rev_comp_mapping_barcod:48,"1766_0111":[178,10],otu_param:7,distinct:[90,1,177,136,195],read_1_id:5,shared_otu:149,program:[1,5,79,78,15,19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basis of sample metadata. Mapping file can also be filtered to the resulting set of sample ids.","<em>pick_open_reference_otus.py</em> –","<em>merge_otu_maps.py</em> – Merge OTU mapping files","<em>parallel_blast.py</em> – Parallel BLAST","<em>upgma_cluster.py</em> – Build a UPGMA tree comparing samples","<em>beta_diversity_metrics</em> – List of available metrics","<em>plot_rank_abundance_graph.py</em> – plot rank-abundance curve","Using usearch quality filtering with QIIME","<em>cytoscape_usage</em> – Visualizing Results with Cytoscape","<em>otu_category_significance.py</em> – OTU significance and co-occurence analysis","<em>plot_taxa_summary.py</em> – Make taxaonomy summary charts based on taxonomy assignment","<em>summarize_taxa.py</em> – Summarize taxa and store results in a new table or appended to an existing mapping file.","<em>convert_unifrac_sample_mapping_to_otu_table.py</em> – Convert a UniFrac sample mapping file to an OTU table","<em>beta_diversity.py</em> – Calculate beta diversity (pairwise sample dissimilarity) on one or many otu tables","<em>alpha_diversity_metrics</em> – List of available metrics","Making Cytoscape Networks","QIIME Developer Notes","<em>jackknifed_beta_diversity.py</em> – A workflow script for performing jackknifed UPGMA clustering and build jackknifed 2d and 3D PCoA plots.","<em>make_otu_heatmap.py</em> – Make heatmap of OTU table","<em>parallel_pick_otus_uclust_ref.py</em> – Parallel pick otus using uclust_ref","Comparing Distance Matrices","<em>make_prefs_file.py</em> – Generate preferences file","<em>multiple_rarefactions_even_depth.py</em> – Perform multiple rarefactions on a single otu table, at one depth of sequences/sample","<em>make_distance_boxplots.py</em> – Creates boxplots to compare distances between categories","<em>plot_semivariogram.py</em> – Fits a model between two distance matrices and plots the result","Taxonomic classifications of single- and paired-end sequences with RTAX","<em>make_3d_plots.py</em> – Make 3D PCoA plots","Filtering contaminant or category specific OTUs from OTU tables","Analysis of 18S data","<em>categorized_dist_scatterplot.py</em> – makes a figure representing average distances between samples, broken down by categories. I call it a ‘categorized distance scatterplot’","<em>single_rarefaction.py</em> – Perform rarefaction on an otu table","<em>quality_scores_plot.py</em> – Generates histograms of sequence quality scores and number of nucleotides recorded at a particular index","<em>make_bootstrapped_tree.py</em> – Make bootstrapped tree","<em>filter_alignment.py</em> – Filter sequence alignment by removing highly variable regions","<em>submit_to_mgrast.py</em> – This script submits a FASTA file to MG-RAST","<em>denoiser_worker.py</em> – Start a denoiser worker process","biom-format table objects","<em>split_libraries_fastq.py</em> – This script performs demultiplexing of Fastq sequence data where barcodes and sequences are contained in two separate fastq files (common on Illumina runs).","QIIME EC2 Image","<em>print_metadata_stats.py</em> – Count the number of samples associated to a category value","<em>parallel_pick_otus_blast.py</em> – Parallel pick otus using BLAST","<em>filter_otus_from_otu_table.py</em> – Filter OTUs from an OTU table based on their observation counts or identifier.","<em>principal_coordinates.py</em> – Principal Coordinates Analysis (PCoA)","<em>collate_alpha.py</em> – Collate alpha diversity results","Fungal ITS analysis tutorial (an IPython Notebook): open-reference OTU picking","<em>compute_core_microbiome.py</em> – Identify the core microbiome.","<em>make_otu_table.py</em> – Make OTU table","<em>compare_3d_plots.py</em> – Plot several PCoA files on the same 3D plot","<em>make_otu_heatmap_html.py</em> – Make heatmap of OTU table","<em>merge_otu_tables.py</em> – Merge two or more OTU tables into a single OTU table.","<em>parallel_pick_otus_trie.py</em> – Parallel pick otus using a trie","<em>inflate_denoiser_output.py</em> – Inflate denoiser results so they can be passed directly to OTU pickers.","<em>cluster_quality.py</em> – compute the quality of a cluster","<em>demultiplex_fasta.py</em> – Demultiplex fasta data according to barcode sequences or data supplied in fasta labels.","<em>beta_significance.py</em> – This script runs any of a set of common tests to determine if a sample is statistically significantly different from another sample","<em>parallel_alpha_diversity.py</em> – Parallel alpha diversity","<em>adjust_seq_orientation.py</em> – Get the reverse complement of all sequences","<em>subsample_fasta.py</em> – Randomly subsample sequences from a given fasta file","<em>tree_compare.py</em> – Compare jackknifed/bootstrapped trees","<em>core_diversity_analyses.py</em> – A workflow for running a core set of QIIME diversity analyses.","Installing QIIME","<em>multiple_rarefactions.py</em> – Perform multiple subsamplings/rarefactions on an otu table","<em>clean_raxml_parsimony_tree.py</em> – Remove duplicate tips from Raxml Tree","<em>check_id_map.py</em> – Checks user’s metadata mapping file for required data, valid format","<em>ampliconnoise.py</em> – Run AmpliconNoise","Report and fixing bugs","<em>distance_matrix_from_mapping.py</em> – Calculate the pairwise dissimilarity on one column of a mappping file","<em>process_sff.py</em> – Convert sff to FASTA and QUAL files","<em>blast_wrapper.py</em> – Blast Interface","<em>print_qiime_config.py</em> – Print out the qiime config settings.","QIIME: Quantitative Insights Into Microbial Ecology","<em>core_qiime_analyses.py</em> – A workflow for running a core set of QIIME analyses.","<em>parallel_pick_otus_usearch61_ref.py</em> – Parallel pick otus using usearch_ref","QIIME Tutorials","<em>consensus_tree.py</em> – This script outputs a majority consensus tree given a collection of input trees.","<em>filter_distance_matrix.py</em> – Filter a distance matrix to contain only a specified set of samples.","<em>supervised_learning.py</em> – Run supervised classification using OTUs as predictors and a mapping file category as class labels.","Denoising and chimera detection usage differences in QIIME","<em>pick_closed_reference_otus.py</em> – Closed-reference OTU picking/Shotgun UniFrac workflow.","Predicting Mislabeled Samples","<em>convert_fastaqual_fastq.py</em> – From a FASTA file and a matching QUAL file, generates a FASTQ file. From FASTQ file generates FASTA file and matching QUAL file.","Upgrading to the latest version of QIIME","QIIME coding guidelines","<em>pick_otus_through_otu_table.py</em> – A workflow script for picking OTUs through building OTU tables","<em>compare_alpha_diversity.py</em> – This script compares alpha diversities based on a two-sample t-test using either parametric or non-parametric (Monte Carlo) methods.","<em>denoiser_preprocess.py</em> – Run phase of denoiser algorithm: prefix clustering","Comparing Categories","Installing QIIME natively","<em>make_fastq.py</em> – Make FASTQ file for ERA submission from paired FASTA and QUAL files","<em>trim_sff_primers.py</em> – Trim sff primers","<em>split_otu_table_by_taxonomy.py</em> – Script to split a single OTU table into multiple tables based on the taxonomy at some user-specified depth.","<em>exclude_seqs_by_blast.py</em> – Exclude contaminated sequences using BLAST","Discussion of subsampled open reference OTU picking in QIIME","<em>truncate_reverse_primer.py</em> – Takes a demultiplexed fasta file, finds a specified reverse primer sequence, and truncates this primer and subsequent sequences following the reverse primer.","QIIME Documentation","<em>parallel_align_seqs_pynast.py</em> – Parallel sequence alignment using PyNAST","<em>make_phylogeny.py</em> – Make Phylogeny","<em>filter_tree.py</em> – This script prunes a tree based on a set of tip names","<em>parallel_assign_taxonomy_blast.py</em> – Parallel taxonomy assignment using BLAST","<em>count_seqs.py</em> –","<em>filter_taxa_from_otu_table.py</em> – Filter taxa from an OTU table","<em>merge_mapping_files.py</em> – Merge mapping files","<em>filter_fasta.py</em> – This script can be applied to remove sequences from a fasta or fastq file based on input criteria.","<em>sort_otu_table.py</em> – Script for sorting the sample IDs in an OTU table based on a specified value in a mapping file.","Preparing raw Illumina data in different formats for use with QIIME","<em>nmds.py</em> – Nonmetric Multidimensional Scaling (NMDS)","Working with BIOM tables in QIIME","<em>make_library_id_lists.py</em> – Make library id lists","<em>truncate_fasta_qual_files.py</em> – Generates filtered fasta and quality score files by truncating at the specified base position.","<em>parallel_multiple_rarefactions.py</em> – Parallel multiple file rarefaction","<em>pick_otus.py</em> – OTU picking","<em>pick_subsampled_reference_otus_through_otu_table.py</em> –","Illumina Overview Tutorial (an IPython Notebook): open reference OTU picking and core diversity analyses","<em>convert_otu_table_to_unifrac_sample_mapping.py</em> – Convert a QIIME OTU table to a UniFrac sample mapping file","<em>start_parallel_jobs_torque.py</em> – Starts multiple jobs in parallel on torque/qsub based multiprocessor systems.","<em>extract_seqs_by_sample_id.py</em> – Extract sequences based on the SampleID","Chimera checking sequences with QIIME","<em>insert_seqs_into_tree.py</em> – Tree Insertion","Multi-step OTU picking","Creating Distance Comparison Plots","Using Remote Mapping Files","<em>add_alpha_to_mapping_file.py</em> – Add alpha diversity data to a metadata mapping file","Denoising of 454 Data Sets","<em>validate_demultiplexed_fasta.py</em> – Checks a fasta file to verify if it has been properly demultiplexed, i.e., it is in QIIME compatible format.","<em>parallel_beta_diversity.py</em> – Parallel beta diversity","Re-training the RDP Classifier","<em>map_reads_to_reference.py</em> – Script for performing assignment of reads against a reference database","Automated script testing","<em>transform_coordinate_matrices.py</em> – Transform 2 coordinate matrices","<em>parallel_map_reads_to_reference.py</em> –","<em>process_qseq.py</em> – Given a directory of per-swath qseq files, this script generates a single fastq per lane.","<em>compare_taxa_summaries.py</em> – Compares taxa summary files","Basic Unix/Linux/OS X commands","<em>make_per_library_sff.py</em> – Make per-library sff files from ID lists","<em>conditional_uncovered_probability.py</em> – Calculate the conditional uncovered probability on each sample in an otu table.","Comparing Taxa Summaries","<em>compare_distance_matrices.py</em> – Computes Mantel correlation tests between sets of distance matrices","<em>split_libraries.py</em> – Split libraries according to barcodes specified in mapping file","<em>shared_phylotypes.py</em> – Compute shared OTUs between all pairs of samples","<em>make_qiime_py_file.py</em> – Create python file","<em>simsam.py</em> – Simulate samples for each sample in an OTU table, using a phylogenetic tree.","<em>make_distance_comparison_plots.py</em> – Creates plots comparing distances between sample groupings","<em>detrend.py</em> – Detrend Principal Coordinates","<em>poller.py</em> – Poller for parallel QIIME scripts.","<em>identify_missing_files.py</em> – This script checks for the existence of expected files in parallel runs.","<em>pick_reference_otus_through_otu_table.py</em> – Reference OTU picking/Shotgun UniFrac workflow.","<em>summarize_otu_by_cat.py</em> – Summarize an OTU table by a single column in the mapping file.","QIIME scripts","Analysis of shotgun sequencing data","<em>summarize_taxa_through_plots.py</em> – A workflow script for performing taxonomy summaries and plots","<em>denoise_wrapper.py</em> – Denoise a flowgram file","<em>load_remote_mapping_file.py</em> – Downloads and saves a remote mapping file","<em>unweight_fasta.py</em> – Transform fasta files with abundance weighting into unweighted","<em>make_qiime_rst_file.py</em> – Make Sphinx RST file","<em>pick_de_novo_otus.py</em> – A workflow for de novo OTU picking, taxonomy assignment, phylogenetic tree construction, and OTU table construction.","<em>fix_arb_fasta.py</em> – Reformat ARB FASTA files","<em>filter_otus_by_sample.py</em> – Filter OTU mapping file and sequences by SampleIDs","<em>split_otu_table.py</em> – Split in a single OTU table into one OTU table per value in a specified field of the mapping file.","<em>compare_categories.py</em> – Analyzes statistical significance of sample groupings using distance matrices","<em>beta_diversity_through_plots.py</em> – A workflow script for computing beta diversity distance matrices and generating PCoA plots","<em>identify_chimeric_seqs.py</em> – Identify chimeric sequences in input FASTA file","<em>alpha_rarefaction.py</em> – A workflow script for performing alpha rarefaction","<em>parallel_assign_taxonomy_rdp.py</em> – Parallel taxonomy assignment using RDP","QIIME parameters files","OTU picking strategies in QIIME","Contributing to QIIME","<em>make_bipartite_network.py</em> – This script makes a bipartite network connecting samples to observations. It is most suitable for visualization with cytoscape.","Input Files","Using parallel QIIME","Describing samples based on their metadata","<em>split_fasta_on_sample_ids.py</em> – Split a single post-split_libraries.py fasta file into per-sample fasta files.","<em>make_distance_histograms.py</em> – Make distance histograms","<em>make_rarefaction_plots.py</em> – Generate Rarefaction Plots","<em>preferences_file</em> – Example of a prefs file","<em>start_parallel_jobs.py</em> – Starts multiple jobs in parallel on multicore or multiprocessor systems.","<em>pick_rep_set.py</em> – Pick representative set of sequences","<em>parallel_identify_chimeric_seqs.py</em> – Parallel chimera detection","<em>dissimilarity_mtx_stats.py</em> – Calculate mean, median and standard deviation from a set of distance matrices","454 Overview Tutorial: de novo OTU picking and diversity analyses using 454 data","<em>relatedness.py</em> – Calculate NRI (net relatedness index) and NTI (nearest taxon index) using the formulas from Phylocom 4.2/3.41 and Webb 2002.","Biological Observation Matrix (biom) format","<em>poller_example.py</em> – Create python file","<em>convert_fastaqual_to_fastq.py</em> – From a FASTA file and a matching QUAL file, generates a minimal FASTQ file.","<em>make_2d_plots.py</em> – Make 2D PCoA Plots","<em>make_otu_network.py</em> – Make an OTU network and calculate statistics","Running Supervised Learning","<em>neighbor_joining.py</em> – Build a neighbor joining tree comparing samples","Working with QIIME on Amazon Web Services EC2","<em>make_tep.py</em> – Makes TopiaryExplorer project file","<em>pool_by_metadata.py</em> – pool samples in OTU table and mapping file based on sample metadata from mapping file","<em>alpha_diversity.py</em> – Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics","<em>start_parallel_jobs_sc.py</em> – Starts parallel jobs on Sun GridEngine queueing systems."],objects:{},titleterms:{represent:191,all:[10,149,98,67],code:[93,98,176],partial:31,make_otu_heatmap_html:59,subsample_fasta:68,signific:[169,20,103],correl:147,upgrad:92,chimeraslay:[88,127,98],follow:104,primer:[100,178,104],preferences_fil:184,hierarch:189,parallel_blast:14,extract_seqs_by_sample_id:126,system:[125,185,202],make_qiime_rst_fil:164,fasta:[64,113,99,91,68,104,181,119,163,36,171,10,166,178,45,78,134,193],compute_core_microbiom:56,matrix:[86,191],deviat:188,sourc:2,cyberduck:198,downstream:115,pcoa:[37,170,159,28,53,58,189,194],pick_de_novo_otu:165,microbi:81,failur:103,blast:[51,79,14,102,109],filter_fasta:113,quantit:81,common:[48,65],microbiom:56,list:[118,16,144,25,81],prefix:96,iter:103,split_otu_table_by_taxonomi:101,round:103,picker:62,merge_otu_t:60,make_fastq:99,version:[98,92],plot_semivariogram:35,biolog:191,video:9,pass:62,download:[162,81],carlo:95,submit:[45,176],parallel_pick_otus_usearch61_ref:83,compat:134,index:[42,190],what:[9,179,103,76,49],parallel_multiple_rarefact:120,plot_taxa_summari:21,compar:[197,31,142,69,34,7,95,97,146,189,152,15],defin:[93,7,136,159],sun:202,summarize_taxa_through_plot:160,current:143,experiment:38,"new":[138,103,136,22],net:190,significantli:65,method:[95,1,129],metadata:[178,180,132,10,11,74,200,117],chimer:171,pick_closed_reference_otu:89,full:[138,129],caveat:131,taxaonomi:21,usag:[18,138,88,2],gener:[32,193,91,141,178,170,159,8,119,189,42,183],uclust_ref:30,bodi:103,gridengin:202,path:[138,98],valu:[50,168,0,114],wait:179,box:9,flowgram:161,denoiser_work:46,rdp:[136,173],correlogram:31,nmd:116,qiime_config:0,submit_to_mgrast:45,queue:202,parallel_assign_taxonomy_blast:109,pick:[121,30,156,103,51,129,83,36,123,94,55,186,189,165,175,61,89],chang:[143,191],compare_taxa_summari:142,appli:113,prefer:[189,32],unix:143,instal:[9,81,98,71,92],taxonom:[189,36],unit:189,highli:44,plot:[159,37,130,17,28,160,35,194,58,189,183,152,170],silva:39,from:[65,111,2,99,91,68,113,52,36,11,38,73,200,3,188,190,144,143,193],describ:180,zip:143,commun:189,pref:184,two:[95,48,35,60],next:129,process_qseq:141,predict:90,call:40,criteria:113,make_2d_plot:194,more:60,sort:[18,117,114],insert_seqs_into_tre:128,filter_otus_by_sampl:167,share:149,cytoscap:[19,177,26],summarize_taxa:22,parallel_pick_otus_uclust_ref:30,usearch:[18,88,175,127,98],train:136,particular:42,make_bootstrapped_tre:43,unpack:98,must:129,beta_diversity_through_plot:170,join:197,discontinu:9,setup:[98,7],work:[198,179,18,138,117,143],can:[113,11,129,62],consensus_tre:85,learn:196,assign_taxonomi:5,control:38,nearest:190,prefilt:103,start_parallel_job:185,make_otu_network:195,process:[46,115,175,103],topiaryexplor:199,clean_raxml_parsimony_tre:73,topic:115,bipartit:177,chimera:[18,88,127,187],convert_unifrac_sample_mapping_to_otu_t:23,tab:[189,2,191],pick_reference_otus_through_otu_t:156,serial:103,contamin:[38,102],occur:20,contribut:176,multipl:[101,185,120,33,72,125,115],filepath:7,make_otu_heatmap:29,anoth:65,classifi:[18,136,36],write:[179,76],how:[18,179,138,131],mapp:77,pair:[115,149,99,146,36],verifi:134,parallel_align_seqs_pynast:106,collaps:159,validate_demultiplexed_fasta:134,heatmap:[189,59,29],core_diversity_analys:70,print_qiime_config:80,split_fasta_on_sample_id:181,compare_distance_matric:147,check_id_map:74,mac:92,notebook:[123,198,55],make_prefs_fil:32,nucleotid:[42,159],end:[115,36],data:[64,48,2,198,132,133,7,159,115,39,3,189,74],parallel:[154,66,30,185,179,51,83,106,103,125,109,187,173,189,155,202,14,61,120,135],averag:40,essenti:189,bootstrap:[189,43,69],exclud:102,inform:98,environ:[179,98,159,7],volum:198,fallback:36,order:175,ssh:198,composit:189,help:[9,176],insight:81,through:[189,94],taxonomi:[101,178,5,160,21,136,173,189,117,165,109],convert_fastaqual_fastq:91,paramet:[178,6,174,136,175],parallel_beta_divers:135,group:[169,152],fit:35,jackknifed_beta_divers:28,fix:[178,76],distance_matrix_from_map:77,start_parallel_jobs_sc:202,window:9,merge_otu_map:13,persist:198,unifrac:[23,124,156,89],pool_by_metadata:200,split_otu_t:168,non:[115,95],thei:62,handl:178,shared_phylotyp:149,initi:7,retrain:136,rank:17,upgma:[189,28,15],introduct:[2,31,130,146,18,97,131,189],parallel_map_reads_to_refer:140,name:[93,10,108],add_qiime_label:10,troubleshoot:[9,136],revers:[104,67],filter_taxa_from_otu_t:111,separ:[39,48,2],mode:[175,103],each:[5,145,36,201,151,189],found:76,truncat:[119,104],mean:188,subset:98,domain:39,weight:163,map:[112,157,168,132,131,129,124,114,162,23,10,11,74,200,22,189,87,13,178,148,167],median:188,related:190,pick_open_reference_otu:12,expect:[155,146],extract:126,out:[198,179,38,80],variabl:[98,159,7,44],given:[68,141,85,8],barcod:[115,64,48,178,148],sourcetrack:2,categori:[50,34,159,38,97,40,87,103],sane:103,suitabl:177,print:80,formula:190,ref:18,matric:[139,31,169,170,35,147,188],statist:[189,169,65,195],workflow:[82,172,156,165,170,70,28,160,94,39,189,175,103,174,89],contain:[86,10,48],map_reads_to_refer:137,free:18,standard:188,nti:190,base:[101,126,18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