├── .gitignore ├── CHANGELOG.md ├── README.md ├── TODO.md ├── bin └── dRep ├── docs ├── Makefile ├── advanced_use.rst ├── choosing_parameters.rst ├── conf.py ├── drep.rst ├── example_output.rst ├── images │ ├── Cluster_scoringK1.png │ ├── Cluster_scoringK2.png │ ├── Cluster_scoringK3.png │ ├── Figure0.jpg │ ├── FigureB.png │ ├── FigureC.png │ ├── FigureD.png │ ├── Primary_cluster_1_average.png │ ├── Primary_clustering_dendrogramK.png │ ├── Secondary_clustering_dendrogramsK.png │ ├── checkM.png │ ├── minANI.png │ ├── subsettingv0.jpg │ ├── subsettingv0.pdf │ └── subsettingv0.png ├── index.rst ├── installation.rst ├── make.bat ├── module_descriptions.rst ├── overview.rst ├── quick_start.rst └── source │ ├── drep.rst │ └── modules.rst ├── drep ├── VERSION ├── WorkDirectory.py ├── __init__.py ├── argumentParser.py ├── controller.py ├── d_adjust.py ├── d_analyze.py ├── d_bonus.py ├── d_choose.py ├── d_cluster │ ├── __init__.py │ ├── cluster_utils.py │ ├── compare_utils.py │ ├── controller.py │ ├── external.py │ ├── greedy_clustering.py │ ├── parsers.py │ └── utils.py ├── d_evaluate.py ├── d_filter.py └── d_workflows.py ├── helper_scripts ├── ScaffoldLevel_dRep.py └── parse_stb.py ├── pyproject.toml ├── requirements.txt ├── setup.py └── tests ├── .DS_Store ├── genomes ├── Enterococcus_casseliflavus_EC20.fasta ├── Enterococcus_faecalis_T2.fna ├── Enterococcus_faecalis_TX0104.fa ├── Enterococcus_faecalis_YI6-1.fna └── Escherichia_coli_Sakai.fna ├── test_backend └── .gitignore ├── test_solutions ├── .DS_Store ├── ecoli_taxonomy │ ├── data │ │ ├── centrifuge │ │ │ ├── Enterococcus_casseliflavus_EC20.fasta_hits.tsv │ │ │ ├── Enterococcus_casseliflavus_EC20.fasta_report.tsv │ │ │ ├── Enterococcus_faecalis_T2.fna_hits.tsv │ │ │ ├── Enterococcus_faecalis_T2.fna_report.tsv │ │ │ ├── Enterococcus_faecalis_TX0104.fa_hits.tsv │ │ │ ├── Enterococcus_faecalis_TX0104.fa_report.tsv │ │ │ ├── Enterococcus_faecalis_YI6-1.fna_hits.tsv │ │ │ ├── Enterococcus_faecalis_YI6-1.fna_report.tsv │ │ │ ├── Escherichia_coli_Sakai.fna_hits.tsv │ │ │ └── Escherichia_coli_Sakai.fna_report.tsv │ │ └── prodigal │ │ │ ├── Enterococcus_casseliflavus_EC20.fasta.faa │ │ │ ├── Enterococcus_casseliflavus_EC20.fasta.fna │ │ │ ├── Enterococcus_faecalis_T2.fna.faa │ │ │ ├── Enterococcus_faecalis_T2.fna.fna │ │ │ ├── Enterococcus_faecalis_TX0104.fa.faa │ │ │ ├── Enterococcus_faecalis_TX0104.fa.fna │ │ │ ├── Enterococcus_faecalis_YI6-1.fna.faa │ │ │ ├── Enterococcus_faecalis_YI6-1.fna.fna │ │ │ ├── Escherichia_coli_Sakai.fna.faa │ │ │ └── Escherichia_coli_Sakai.fna.fna │ ├── data_tables │ │ ├── Bdb.csv │ │ ├── BdbP.csv │ │ ├── Tdb.csv │ │ └── TdbP.csv │ └── log │ │ └── logger.log └── ecoli_wd │ ├── .DS_Store │ ├── data │ ├── ANImf_files │ │ ├── Enterococcus_casseliflavus_EC20.fasta_vs_Enterococcus_casseliflavus_EC20.fasta.delta │ │ ├── Enterococcus_casseliflavus_EC20.fasta_vs_Enterococcus_casseliflavus_EC20.fasta.delta.filtered │ │ ├── Enterococcus_faecalis_T2.fna_vs_Enterococcus_faecalis_T2.fna.delta │ │ ├── Enterococcus_faecalis_T2.fna_vs_Enterococcus_faecalis_T2.fna.delta.filtered │ │ ├── Enterococcus_faecalis_T2.fna_vs_Enterococcus_faecalis_TX0104.fa.delta │ │ ├── Enterococcus_faecalis_T2.fna_vs_Enterococcus_faecalis_TX0104.fa.delta.filtered │ │ ├── Enterococcus_faecalis_T2.fna_vs_Enterococcus_faecalis_YI6-1.fna.delta │ │ ├── Enterococcus_faecalis_T2.fna_vs_Enterococcus_faecalis_YI6-1.fna.delta.filtered │ │ ├── Enterococcus_faecalis_TX0104.fa_vs_Enterococcus_faecalis_T2.fna.delta │ │ ├── Enterococcus_faecalis_TX0104.fa_vs_Enterococcus_faecalis_T2.fna.delta.filtered │ │ ├── Enterococcus_faecalis_TX0104.fa_vs_Enterococcus_faecalis_TX0104.fa.delta │ │ ├── Enterococcus_faecalis_TX0104.fa_vs_Enterococcus_faecalis_TX0104.fa.delta.filtered │ │ ├── Enterococcus_faecalis_TX0104.fa_vs_Enterococcus_faecalis_YI6-1.fna.delta │ │ ├── Enterococcus_faecalis_TX0104.fa_vs_Enterococcus_faecalis_YI6-1.fna.delta.filtered │ │ ├── Enterococcus_faecalis_YI6-1.fna_vs_Enterococcus_faecalis_T2.fna.delta │ │ ├── Enterococcus_faecalis_YI6-1.fna_vs_Enterococcus_faecalis_T2.fna.delta.filtered │ │ ├── Enterococcus_faecalis_YI6-1.fna_vs_Enterococcus_faecalis_TX0104.fa.delta │ │ ├── Enterococcus_faecalis_YI6-1.fna_vs_Enterococcus_faecalis_TX0104.fa.delta.filtered │ │ ├── Enterococcus_faecalis_YI6-1.fna_vs_Enterococcus_faecalis_YI6-1.fna.delta │ │ ├── Enterococcus_faecalis_YI6-1.fna_vs_Enterococcus_faecalis_YI6-1.fna.delta.filtered │ │ ├── Escherichia_coli_Sakai.fna_vs_Escherichia_coli_Sakai.fna.delta │ │ └── Escherichia_coli_Sakai.fna_vs_Escherichia_coli_Sakai.fna.delta.filtered │ ├── ANIn_files │ │ ├── Enterococcus_casseliflavus_EC20.fasta_vs_Enterococcus_casseliflavus_EC20.fasta.delta │ │ ├── Enterococcus_faecalis_T2.fna_vs_Enterococcus_faecalis_T2.fna.delta │ │ ├── Enterococcus_faecalis_T2.fna_vs_Enterococcus_faecalis_TX0104.fa.delta │ │ ├── Enterococcus_faecalis_T2.fna_vs_Enterococcus_faecalis_YI6-1.fna.delta │ │ ├── Enterococcus_faecalis_TX0104.fa_vs_Enterococcus_faecalis_T2.fna.delta │ │ ├── Enterococcus_faecalis_TX0104.fa_vs_Enterococcus_faecalis_TX0104.fa.delta │ │ ├── Enterococcus_faecalis_TX0104.fa_vs_Enterococcus_faecalis_YI6-1.fna.delta │ │ ├── Enterococcus_faecalis_YI6-1.fna_vs_Enterococcus_faecalis_T2.fna.delta │ │ ├── Enterococcus_faecalis_YI6-1.fna_vs_Enterococcus_faecalis_TX0104.fa.delta │ │ ├── Enterococcus_faecalis_YI6-1.fna_vs_Enterococcus_faecalis_YI6-1.fna.delta │ │ └── Escherichia_coli_Sakai.fna_vs_Escherichia_coli_Sakai.fna.delta │ ├── Clustering_files │ │ ├── primary_linkage.pickle │ │ └── secondary_linkage_cluster_1.pickle │ ├── MASH_files │ │ ├── ALL.msh │ │ ├── MASH_table.tsv │ │ └── sketches │ │ │ ├── Enterococcus_casseliflavus_EC20.fasta.msh │ │ │ ├── Enterococcus_faecalis_T2.fna.msh │ │ │ ├── Enterococcus_faecalis_TX0104.fa.msh │ │ │ ├── Enterococcus_faecalis_YI6-1.fna.msh │ │ │ └── Escherichia_coli_Sakai.fna.msh │ ├── checkM │ │ └── checkM_outdir │ │ │ ├── Bacteria.ms │ │ │ ├── Chdb.tsv │ │ │ ├── bins │ │ │ ├── Enterococcus_casseliflavus_EC20.fasta │ │ │ │ ├── genes.faa │ │ │ │ └── hmmer.analyze.txt │ │ │ ├── Enterococcus_faecalis_T2.fna │ │ │ │ ├── genes.faa │ │ │ │ └── hmmer.analyze.txt │ │ │ ├── Enterococcus_faecalis_TX0104.fa │ │ │ │ ├── genes.faa │ │ │ │ └── hmmer.analyze.txt │ │ │ ├── Enterococcus_faecalis_YI6-1.fna │ │ │ │ ├── genes.faa │ │ │ │ └── hmmer.analyze.txt │ │ │ └── Escherichia_coli_Sakai.fna │ │ │ │ ├── genes.faa │ │ │ │ └── hmmer.analyze.txt │ │ │ ├── results.tsv │ │ │ └── storage │ │ │ ├── bin_stats.analyze.tsv │ │ │ ├── bin_stats_ext.tsv │ │ │ ├── checkm_hmm_info.pkl.gz │ │ │ └── marker_gene_stats.tsv │ └── prodigal │ │ ├── Enterococcus_casseliflavus_EC20.fasta.faa │ │ ├── Enterococcus_casseliflavus_EC20.fasta.fna │ │ ├── Enterococcus_faecalis_T2.fna.faa │ │ ├── Enterococcus_faecalis_T2.fna.fna │ │ ├── Enterococcus_faecalis_TX0104.fa.faa │ │ ├── Enterococcus_faecalis_TX0104.fa.fna │ │ ├── Enterococcus_faecalis_YI6-1.fna.faa │ │ ├── Enterococcus_faecalis_YI6-1.fna.fna │ │ ├── Escherichia_coli_Sakai.fna.faa │ │ └── Escherichia_coli_Sakai.fna.fna │ ├── data_tables │ ├── Bdb.csv │ ├── Cdb.csv │ ├── Chdb.csv │ ├── Mdb.csv │ ├── Ndb.csv │ ├── Sdb.csv │ ├── Wdb.csv │ ├── Widb.csv │ └── genomeInformation.csv │ └── log │ ├── amiinsane.txt │ ├── cluster_arguments.json │ ├── cmd_logs │ ├── 2017-10-24_15.05.37.503502.CMD │ ├── 2017-10-24_15.05.37.503502.STDERR │ ├── 2017-10-24_15.05.37.503502.STDOUT │ ├── 2017-10-24_15.05.37.513196.CMD │ ├── 2017-10-24_15.05.37.513196.STDERR │ ├── 2017-10-24_15.05.37.513196.STDOUT │ ├── 2017-10-24_15.05.37.559264.CMD │ ├── 2017-10-24_15.05.37.559264.STDERR │ ├── 2017-10-24_15.05.37.559264.STDOUT │ ├── 2017-10-24_15.05.42.429566.CMD │ ├── 2017-10-24_15.05.42.429566.STDERR │ ├── 2017-10-24_15.05.42.429566.STDOUT │ ├── 2017-10-24_15.05.42.429684.CMD │ ├── 2017-10-24_15.05.42.429684.STDERR │ ├── 2017-10-24_15.05.42.429684.STDOUT │ ├── 2017-10-24_15.05.42.430026.CMD │ ├── 2017-10-24_15.05.42.430026.STDERR │ ├── 2017-10-24_15.05.42.430026.STDOUT │ ├── 2017-10-24_15.05.42.430055.CMD │ ├── 2017-10-24_15.05.42.430055.STDERR │ ├── 2017-10-24_15.05.42.430055.STDOUT │ ├── 2017-10-24_15.05.42.430322.CMD │ ├── 2017-10-24_15.05.42.430322.STDERR │ ├── 2017-10-24_15.05.42.430322.STDOUT │ ├── 2017-10-24_15.05.42.430485.CMD │ ├── 2017-10-24_15.05.42.430485.STDERR │ ├── 2017-10-24_15.05.42.430485.STDOUT │ ├── 2017-10-24_15.05.42.430749.CMD │ ├── 2017-10-24_15.05.42.430749.STDERR │ ├── 2017-10-24_15.05.42.430749.STDOUT │ ├── 2017-10-24_15.05.42.431007.CMD │ ├── 2017-10-24_15.05.42.431007.STDERR │ ├── 2017-10-24_15.05.42.431007.STDOUT │ ├── 2017-10-24_15.05.42.431077.CMD │ ├── 2017-10-24_15.05.42.431077.STDERR │ ├── 2017-10-24_15.05.42.431077.STDOUT │ ├── 2017-10-24_15.05.50.491219.CMD │ ├── 2017-10-24_15.05.50.491219.STDERR │ └── 2017-10-24_15.05.50.491219.STDOUT │ └── logger.log ├── test_suite.py └── tests ├── __init__.py ├── test_analyze.py ├── test_bonus.py ├── 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