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searchindex.js
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Search.setIndex({envversion:42,terms:{line_color:[169,33],aln:[134,131],c__erysipelotrichi:183,entropi:[38,43],orthogon:183,whatev:9,box_color:32,"_log":1,yellow:[183,30,171,25],confidence_level:[136,114],four:[133,63,98,172,173,174,118,151,139,140,141,130,183],secondli:173,prefix:[63,94,1,127,3],rolhf:160,seconds_to_sleep:[0,65,134,16,117,50,81,156,73,105,181,166,80,28,94,14,60],fig1:39,dist:[93,182],de_novo_chimera_detect:[18,118],consider:[183,128,160,172],whose:[169,160,121,189,43,37,180,184],specificcalcul:36,lgpl:94,jobs_to_start:[0,65,69,119,73,14,157,165,117,163,81,166,87,28,174,105,181,80,12,94,134,50,156,60],spacedefault:112,aug:[18,94],tail_typ:[136,140,145,32],not_barcod:171,abundance_skew:[18,118],collated_alpha:[91,53],deviat:91,weighted_normalized_unifrac:64,under:[63,169,160,79,191,174,128,91,20,141,180,167,94,171,114],preprocess:[92,128,3],slowest:128,unassembl:44,worth:128,suitabl:150,creating_distance_comparison_plot:[145,32],lack:[173,5,188],everi:[63,2,29,191,193,125,128,139,35,43,52,21,130,112,183,186,190,53,145,25,15],quantil:127,downstream:[63,79,173,122,118,128,34,141,103,38,3,144,86,168,99],gg_otus_4feb2011:[136,139,35,191,130,111,24],pick_de_novo_otu:[173,150,102,132,94,61],tcttgtattaatcttcctttcagaaggctgtccaagagtagacggcaggttggatacgtgttactcacccgg:18,internet:[9,94,126],biometri:160,individual_id_categori:169,hardwar:9,sl_rarefied_tables_cv10:85,s_8_map:111,govern:128,appar:188,install_script:94,lefthand:126,node_instance_typ:191,f__veillonellacea:99,aaaaaaaa:111,split_library_run1_output:141,school:79,make_bipartite_network:150,prefix_picked_otu:124,xyz:172,sorted_sample_ids_fp:110,unsubsambl:119,"607_1118":124,vector:36,technolog:[63,128,7,141,74,9],pd_whole_tree_alpha:127,sleep:[65,134,16,117,50,81,128,80,73,105,181,166,156,28,14,60],qual_score_window:141,straight:[191,174],filtered_align:43,merge_otu_t:150,g__serratia:130,speci:[79,165,36,118,128,38,130,183,99,114],miller:[118,151],naiv:5,variable_size_distance_class:140,seper:63,direct:[183,94,169,141,25],sturg:[140,29],sourceforg:[38,33,32],outputpath:98,consequ:94,second:[63,0,65,181,5,124,7,188,111,147,73,14,186,80,16,191,117,118,81,164,166,125,28,29,173,31,127,128,34,35,91,105,130,183,41,185,134,49,50,129,139,156,140,136,141,57,60],fece:7,friendlyq:[94,20],chen:36,panda:94,n_taxa_to_keep:183,even:[88,165,160,99,125,131,69,128,7,151,189,141,37,142,93,117,183,85,60,102,163],supervis:[94,150],parallel_multiple_rarefact:150,"454reads_1":3,ttgggccgtgtctcagtcccaatgtggccgtccgccctctc:183,truncate_onli:[183,141,100,128],accgcagagtca:[183,173,37,126],neg:[107,29,160,136,162,27,139,11,58,159],samples_to_keep:11,conduct:64,"new":26,symmetr:[146,162,177,140,32,145],ever:[191,99],happi:111,metadata:185,deflin:103,ongo:38,pick_closed_reference_otu:[94,150,102],subtre:104,jre1:94,"27f":171,displai:[160,36,33,188,120,58,54,37,21,57,183,171],no_single_ok_gener:5,accagacgatgctacgtagggggcaagcgttgtccggatttattgggcgtaaagcgcgtgtaggcggccaggtaggtccgttgtgaaaactggaggcttaac:111,never:[45,191,141],ellipisoid:[36,187],here:[65,2,181,5,6,69,151,7,105,183,73,132,113,14,157,114,79,80,165,160,191,120,118,81,185,18,166,167,23,24,175,25,87,88,68,28,29,173,174,125,162,128,35,111,37,38,93,130,9,12,94,86,133,46,168,109,99,50,139,156,54,171,117,60,180],src_fasttre:94,met:[111,160],added_demultiplex_field:[63,141,171],accur:[88,94,138,35],parameter_fp:[165,163,69,119,152,74,12,157,87],jstjohn:44,interpret:[183,175,29],forens:93,forum:[111,79,94,48,82],correlogram:140,"_636":[183,173,37,126],src_uclust:94,phylogenet:[79,64,65,165,150,163,69,119,188,103,193,112,80,132,23,169],precis:[138,35],master_pcoa:[36,187],cogent:77,trie_reverse_seq:118,sjn:111,expected_out_fp:148,lanemask:[0,157,43,38,183,132,94,122],permit:1,denovootu34054:99,studi:[63,2,7,183,142,113,114,161,126,168,25,88,29,173,125,128,177,93,111,185,188,139,141,103,99],jackknife_sampl:42,unweighted_unifrac_pc_3d_pcoa_plot:[111,99],seqs1:[12,10,99,61,128],seqs2:[12,10,99,61,128],max_walltim:20,julia:79,strap:160,brought:48,bashrc:94,unix:82,verbose_process_run_results_f:186,expected_out_fil:[174,148],moran:162,org:[1,165,136,5,163,69,140,173,10,74,193,162,94,185,114],suppress_primer_check:129,"60_sorted_and_fil":139,txt:[1,2,3,4,5,27,7,8,10,11,13,15,16,17,20,21,22,25,28,29,31,32,33,34,35,37,38,39,40,12,42,43,47,49,50,51,52,53,55,56,57,58,99,102,62,63,64,69,142,73,74,75,84,85,86,87,88,91,92,93,94,96,60,100,61,104,105,106,108,109,110,112,165,117,118,119,36,122,123,124,125,126,127,128,129,130,132,133,30,136,138,139,140,141,144,145,146,147,148,149,121,151,152,153,154,158,159,160,161,162,163,164,166,168,171,172,173,174,175,177,178,169,180,181,111,184,186,187,188,189,190,192,193,194],f__sinobacteracea:99,unit:[79,2,172,118,143,38,32,9,132,94,145,186],highli:[173,46,94,79],refseqs_nt:[134,131],plot:[94,165],dna:[183,173,171,131],describ:[96,0,169,29,90,173,121,118,124,34,82,184,162,141,11,22,86,122,94,172],would:[146,63,181,36,69,151,7,43,40,10,111,189,113,114,79,160,118,18,164,21,22,86,23,175,25,88,123,29,173,174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up your qiime_config file","<em>align_seqs.py</em> – Align sequences using a variety of alignment methods","Tracking the source of microbes with SourceTracker","<em>denoiser.py</em> – Remove noise from 454 sequencing data","<em>trflp_file_to_otu_table.py</em> – Convert TRFLP text file to an OTU table","<em>assign_taxonomy.py</em> – Assign taxonomy to each sequence","Scripts - Analyses and Parameters","Performing Procrustes Analysis","<em>process_iseq.py</em> – Given a directory of per-swath qseq files, this script generates a single fastq per lane.","QIIME Virtual Box","<em>add_qiime_labels.py</em> – Takes a directory, a metadata mapping file, and a column name that contains the fasta file names that SampleIDs are associated with, combines all files that have valid fasta extensions into a single fasta file, with valid QIIME fasta labels.","<em>filter_samples_from_otu_table.py</em> – Filters samples from an OTU table on the basis of the number of observations in that sample, or on the 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>parallel_merge_otu_tables.py</em> – Parallel merge BIOM tables","<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>start_parallel_jobs_torque.py</em> – Starts multiple jobs in parallel on torque/qsub based multiprocessor systems.","<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>beta_diversity.py</em> – Calculate beta diversity (pairwise sample dissimilarity) on one or many otu tables","Basic Unix/Linux/OS X commands","Making Cytoscape Networks","QIIME Developer Notes","<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>extract_barcodes.py</em> – This script is designed to format fastq sequence and barcode data so they are compatible with split_libraries_fastq.py (see http://qiime.org/tutorials/processing_illumina_data.html).","<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","Extracting Barcodes from fastq data for compatibility with <cite>split_libraries_fastq.py</cite>","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>join_paired_ends.py</em> – Joins paired-end Illumina reads.","<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>parallel_assign_taxonomy_uclust.py</em> – Parallel taxonomy assignment using the uclust consensus taxonomy assignment","<em>ampliconnoise.py</em> – Run AmpliconNoise","<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>parallel_beta_diversity.py</em> – Parallel beta diversity","<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","<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","QIIME installation guide","<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","QIIME parameters files","<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>estimate_observation_richness.py</em> – Estimates the observation (e.g., OTU) richness of samples in a BIOM table","<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>jackknifed_beta_diversity.py</em> – A workflow script for performing jackknifed UPGMA clustering and build jackknifed 2d and 3D PCoA plots.","Illumina Overview Tutorial (an IPython Notebook): open reference OTU picking and core diversity analyses","<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.","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 two or more 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","<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>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>parallel_align_seqs_pynast.py</em> – Parallel sequence alignment using PyNAST","<em>pick_de_novo_otus.py</em> – A workflow for de novo OTU picking, taxonomy assignment, phylogenetic tree construction, and OTU table construction.","<em>start_parallel_jobs.py</em> – Starts multiple jobs in parallel on multicore or multiprocessor systems.","<em>filter_otus_by_sample.py</em> – Filter OTU mapping file and sequences by SampleIDs","<no title>","<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","<em>submit_to_mgrast.py</em> – This script submits a FASTA file to MG-RAST","OTU picking strategies in QIIME","<em>identify_paired_differences.py</em> – Generate plots and stats to test for change in some data point(s) with a state change on a per-individual basis.","<em>multiple_rarefactions_even_depth.py</em> – Perform multiple rarefactions on a single otu table, at one depth of sequences/sample","<em>validate_mapping_file.py</em> – Checks user’s metadata mapping file for required data, valid format","<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>fix_arb_fasta.py</em> – Reformat ARB FASTA files","<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>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>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:{split_otu_table_by_taxonomi:97,represent:185,all:[10,142,66],partial:29,make_otu_heatmap_html:58,subsample_fasta:67,signific:[162,99],correl:140,upgrad:90,chimeraslay:[86,122,94],follow:100,primer:[96,173,100],hierarch:183,parallel_blast:14,extract_seqs_by_sample_id:121,fasta:[63,109,95,89,67,100,176,10,155,35,164,116,179,173,167,76,129],compute_core_microbiom:55,deviat:182,sourc:2,cyberduck:191,downstream:111,pcoa:[36,163,151,119,52,57,183,187],pick_de_novo_otu:157,microbi:79,failur:99,blast:[50,77,14,98,105],filter_fasta:109,quantit:79,common:[47,64],microbiom:55,list:[115,79,137],prefix:92,iter:99,sane:99,round:99,picker:61,merge_otu_t:59,make_fastq:95,version:[94,90],plot_semivariogram:33,biolog:185,design:31,pass:61,download:[154,79],carlo:91,submit:167,parallel_pick_otus_usearch61_ref:81,compat:[31,129,34],index:[41,184,34],what:[9,174,99,48],parallel_multiple_rarefact:117,plot_taxa_summari:21,compar:[190,29,136,68,32,7,91,93,139,183,145,15],truncate_fasta_qual_fil:116,sun:194,workflow:[165,157,163,69,119,152,38,183,94,168,99,102,87],summarize_taxa_through_plot:152,current:24,experiment:37,"new":[132,99,130,22],net:184,method:[91,1,124],metadata:[173,175,127,10,11,113,171],chimer:164,pick_closed_reference_otu:87,full:[132,94,124],caveat:126,taxaonomi:21,gener:[169,30,89,135,173,163,151,8,116,183,41,178],uclust_ref:28,bodi:99,gridengin:194,path:[132,94],valu:[49,161,0,110],wait:174,box:9,flowgram:153,denoiser_work:45,rdp:[130,166],correlogram:29,nmd:112,qiime_config:0,submit_to_mgrast:167,queue:194,parallel_assign_taxonomy_blast:105,pick:[118,28,99,50,124,81,35,120,54,180,183,157,168,60,87],chang:[169,24,185],compare_taxa_summari:136,via:94,appli:109,prefer:30,expect:[148,139],unix:24,join_paired_end:44,instal:[9,79,94,70,90],taxonom:[183,35],unit:183,highli:43,plot:[151,169,36,125,17,119,152,33,187,57,183,178,145,163],silva:38,from:[64,107,2,95,89,67,109,51,34,35,11,37,72,3,182,184,137,24],describ:175,zip:24,commun:183,two:[133,47,33,34,91,59],next:124,predict:88,call:39,criteria:109,make_2d_plot:187,more:[133,59],sort:[18,113,110],rdp_jar_path:94,filter_otus_by_sampl:159,share:142,cytoscap:[19,172,25],summarize_taxa:22,parallel_pick_otus_uclust_ref:28,usearch:[18,86,168,122,94],train:130,particular:41,make_bootstrapped_tre:42,unpack:94,must:124,beta_diversity_through_plot:163,join:[44,190],discontinu:9,setup:[94,7],work:[191,174,18,132,113,24],can:[109,11,124,61],consensus_tre:83,learn:[79,189],assign_taxonomi:5,obtain:35,control:37,nearest:184,start_parallel_job:158,make_otu_network:188,process:[45,34,111,94,168,99],topiaryexplor:192,clean_raxml_parsimony_tre:72,topic:111,bipartit:172,chimera:[18,86,122,181],tab:[183,2,185],serial:99,contamin:[37,98],end:[111,44,34,35],filepath:7,make_otu_heatmap:27,anoth:64,classifi:[18,130,35],write:174,how:[18,174,94,132,126],mapp:75,pair:[95,139,35,142,111,44],verifi:129,parallel_align_seqs_pynast:156,collaps:151,validate_demultiplexed_fasta:129,heatmap:[183,58,27],core_diversity_analys:69,print_qiime_config:78,split_fasta_on_sample_id:176,compare_distance_matric:140,pythonpath:94,mac:[94,90],notebook:[120,191,54],make_prefs_fil:30,nucleotid:[41,151],multipl:[97,158,117,170,71,20,111],data:[63,47,169,2,191,31,127,128,34,151,111,38,7,3,183,94,171],parallel:[65,148,80,147,73,14,158,16,117,81,20,166,28,174,105,181,183,60,50,156,99,194],averag:39,essenti:183,bootstrap:[183,42,68],exclud:98,inform:94,combin:10,volum:191,fallback:35,order:168,ssh:191,composit:183,help:9,insight:79,through:183,taxonomi:[97,173,5,152,73,21,130,166,183,113,157,105],convert_fastaqual_fastq:89,paramet:[173,6,130,94,168,102],parallel_beta_divers:80,group:[162,145],fit:33,jackknifed_beta_divers:119,fix:173,distance_matrix_from_map:75,start_parallel_jobs_sc:194,window:9,html:31,merge_otu_map:13,persist:191,mail:79,split_otu_t:161,non:[111,91,94],thei:[31,61],handl:173,shared_phylotyp:142,initi:7,retrain:130,single_rarefact:40,upgma:[183,119,15],introduct:[2,29,125,34,18,139,93,126,183],parallel_map_reads_to_refer:134,name:[10,104],add_qiime_label:10,troubleshoot:[9,130],revers:[100,66],filter_taxa_from_otu_t:107,separ:[38,47,2],exampl:[111,168,102],mode:[168,99],each:[5,138,34,35,193,144,183],truncat:[116,100],mean:182,domain:38,macqiim:94,map:[108,149,161,127,126,124,141,110,154,173,10,11,22,183,85,13,171,159],median:182,individu:169,related:184,pick_open_reference_otu:12,ec2:[191,48],extract:[121,34],out:[191,174,37,78],variabl:[94,151,7,43],given:[67,135,83,8],matrix:[84,185],sourcetrack:2,categori:[49,32,151,37,93,39,85,99],prefilt:99,suitabl:172,print:78,formula:184,ref:18,matric:[133,29,162,163,33,140,182],statist:[183,162,64,188],advanc:94,map_reads_to_refer:131,free:18,standard:[94,182],nti:184,base:[97,121,175,109,51,91,110,18,116,20,21,183,94,104],inflat:61,releas:94,org:31,basi:[11,169],torqu:20,launch:191,upgma_clust:15,keep:24,filter:[2,159,84,107,51,43,18,111,116,37,183,113,99,11],barcod:[63,47,173,31,34,141,111],length:18,anosim:93,neighbor_joi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