├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── config.yml ├── no-response.yml └── workflows │ ├── main.yml │ ├── python-publish.yml │ └── pythonpackage.yml ├── .gitmodules ├── CHANGELOG.md ├── README.md ├── bioconda_recipe └── meta.yaml ├── license.txt ├── metaphlan ├── __init__.py ├── metaphlan.py ├── metaphlan_databases │ └── README.txt ├── strainphlan.py └── utils │ ├── VallesColomerM_2022_Jan21_thresholds.tsv │ ├── VallesColomerM_2022_Nov19_thresholds.tsv │ ├── __init__.py │ ├── add_metadata_tree.py │ ├── calculate_diversity.R │ ├── consensus_markers.py │ ├── create_toy_database.py │ ├── database_controller.py │ ├── external_exec.py │ ├── extract_markers.py │ ├── fix_relab_mpa4.py │ ├── merge_metaphlan_tables.py │ ├── merge_vsc_tables.py │ ├── metaphlan2krona.py │ ├── mpa_vJan21_CHOCOPhlAnSGB_202103_SGB2GTDB.tsv │ ├── mpa_vJan21_CHOCOPhlAnSGB_202103_size.txt.bz2 │ ├── mpa_vJan25_CHOCOPhlAnSGB_202503_SGB2GTDB.tsv │ ├── mpa_vJan25_CHOCOPhlAnSGB_202503_size.txt.bz2 │ ├── mpa_vJun23_CHOCOPhlAnSGB_202307_SGB2GTDB.tsv │ ├── mpa_vJun23_CHOCOPhlAnSGB_202307_size.txt.bz2 │ ├── mpa_vJun23_CHOCOPhlAnSGB_202403_SGB2GTDB.tsv │ ├── mpa_vJun23_CHOCOPhlAnSGB_202403_size.txt.bz2 │ ├── mpa_vOct22_CHOCOPhlAnSGB_202212_SGB2GTDB.tsv │ ├── mpa_vOct22_CHOCOPhlAnSGB_202212_size.txt.bz2 │ ├── oct22_fix_tax.tsv │ ├── parallelisation.py │ ├── phylophlan_controller.py │ ├── plot_bug.py │ ├── plot_tree_graphlan.py │ ├── pyphlan.py │ ├── read_fastx.py │ ├── sample2markers.py │ ├── sgb_to_gtdb_profile.py │ ├── strain_transmission.py │ ├── treeshrink │ ├── .Rhistory │ ├── R_scripts │ │ ├── Rfunctions.R │ │ ├── find_d.R │ │ ├── find_outliers.R │ │ ├── find_outliers_IQR.R │ │ ├── find_outliers_IQR.log.R │ │ ├── find_outliers_adjIQR.R │ │ ├── find_outliers_bootliers.R │ │ ├── find_threshold.R │ │ ├── find_threshold_IQR.R │ │ ├── find_threshold_hnorm.R │ │ ├── find_threshold_kernel.R │ │ ├── find_threshold_lkernel.R │ │ ├── find_threshold_lnorm.R │ │ ├── find_threshold_loglnorm.R │ │ ├── plot_allgenes.R │ │ ├── plot_pergene.R │ │ ├── plot_perspecies.R │ │ └── plot_threshold.R │ ├── Rlib │ │ └── BMS │ │ │ ├── CITATION │ │ │ ├── DESCRIPTION │ │ │ ├── INDEX │ │ │ ├── Meta │ │ │ ├── Rd.rds │ │ │ ├── data.rds │ │ │ ├── demo.rds │ │ │ ├── features.rds │ │ │ ├── hsearch.rds │ │ │ ├── links.rds │ │ │ ├── nsInfo.rds │ │ │ ├── package.rds │ │ │ └── vignette.rds │ │ │ ├── NAMESPACE │ │ │ ├── R │ │ │ ├── BMS │ │ │ ├── BMS.rdb │ │ │ └── BMS.rdx │ │ │ ├── data │ │ │ └── datafls.rda │ │ │ ├── demo │ │ │ └── BMS.growth.R │ │ │ ├── doc │ │ │ ├── bmasmall.bib │ │ │ ├── bms.R │ │ │ ├── bms.Rnw │ │ │ ├── bms.pdf │ │ │ └── index.html │ │ │ ├── help │ │ │ ├── AnIndex │ │ │ ├── BMS.rdb │ │ │ ├── BMS.rdx │ │ │ ├── aliases.rds │ │ │ └── paths.rds │ │ │ └── html │ │ │ ├── 00Index.html │ │ │ └── R.css │ ├── run_treeshrink.py │ ├── scripts │ │ ├── Tree_extend.py │ │ ├── __init__.py │ │ ├── alignment.py │ │ ├── decompose_lib.py │ │ ├── filemgr.py │ │ ├── filter_lib.py │ │ ├── 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