README.md
setup.py
MetaPhlAn.egg-info/PKG-INFO
MetaPhlAn.egg-info/SOURCES.txt
MetaPhlAn.egg-info/dependency_links.txt
MetaPhlAn.egg-info/entry_points.txt
MetaPhlAn.egg-info/requires.txt
MetaPhlAn.egg-info/top_level.txt
metaphlan/__init__.py
metaphlan/metaphlan.py
metaphlan/strainphlan.py
metaphlan/metaphlan_databases/README.txt
metaphlan/utils/VallesColomerM_2022_Jan21_thresholds.tsv
metaphlan/utils/VallesColomerM_2022_Nov19_thresholds.tsv
metaphlan/utils/__init__.py
metaphlan/utils/add_metadata_tree.py
metaphlan/utils/calculate_diversity.R
metaphlan/utils/consensus_markers.py
metaphlan/utils/create_toy_database.py
metaphlan/utils/database_controller.py
metaphlan/utils/external_exec.py
metaphlan/utils/extract_markers.py
metaphlan/utils/fix_relab_mpa4.py
metaphlan/utils/merge_metaphlan_tables.py
metaphlan/utils/merge_vsc_tables.py
metaphlan/utils/metaphlan2krona.py
metaphlan/utils/mpa_vJan21_CHOCOPhlAnSGB_202103_SGB2GTDB.tsv
metaphlan/utils/mpa_vJan21_CHOCOPhlAnSGB_202103_size.txt.bz2
metaphlan/utils/mpa_vJan25_CHOCOPhlAnSGB_202503_SGB2GTDB.tsv
metaphlan/utils/mpa_vJan25_CHOCOPhlAnSGB_202503_size.txt.bz2
metaphlan/utils/mpa_vJun23_CHOCOPhlAnSGB_202307_SGB2GTDB.tsv
metaphlan/utils/mpa_vJun23_CHOCOPhlAnSGB_202307_size.txt.bz2
metaphlan/utils/mpa_vJun23_CHOCOPhlAnSGB_202403_SGB2GTDB.tsv
metaphlan/utils/mpa_vJun23_CHOCOPhlAnSGB_202403_size.txt.bz2
metaphlan/utils/mpa_vOct22_CHOCOPhlAnSGB_202212_SGB2GTDB.tsv
metaphlan/utils/mpa_vOct22_CHOCOPhlAnSGB_202212_size.txt.bz2
metaphlan/utils/oct22_fix_tax.tsv
metaphlan/utils/parallelisation.py
metaphlan/utils/phylophlan_controller.py
metaphlan/utils/plot_bug.py
metaphlan/utils/plot_tree_graphlan.py
metaphlan/utils/pyphlan.py
metaphlan/utils/read_fastx.py
metaphlan/utils/sample2markers.py
metaphlan/utils/sgb_to_gtdb_profile.py
metaphlan/utils/strain_transmission.py
metaphlan/utils/util_fun.py
metaphlan/utils/treeshrink/run_treeshrink.py
metaphlan/utils/treeshrink/treeshrink.py
metaphlan/utils/treeshrink/R_scripts/Rfunctions.R
metaphlan/utils/treeshrink/R_scripts/find_d.R
metaphlan/utils/treeshrink/R_scripts/find_outliers.R
metaphlan/utils/treeshrink/R_scripts/find_outliers_IQR.R
metaphlan/utils/treeshrink/R_scripts/find_outliers_IQR.log.R
metaphlan/utils/treeshrink/R_scripts/find_outliers_adjIQR.R
metaphlan/utils/treeshrink/R_scripts/find_outliers_bootliers.R
metaphlan/utils/treeshrink/R_scripts/find_threshold.R
metaphlan/utils/treeshrink/R_scripts/find_threshold_IQR.R
metaphlan/utils/treeshrink/R_scripts/find_threshold_hnorm.R
metaphlan/utils/treeshrink/R_scripts/find_threshold_kernel.R
metaphlan/utils/treeshrink/R_scripts/find_threshold_lkernel.R
metaphlan/utils/treeshrink/R_scripts/find_threshold_lnorm.R
metaphlan/utils/treeshrink/R_scripts/find_threshold_loglnorm.R
metaphlan/utils/treeshrink/R_scripts/plot_allgenes.R
metaphlan/utils/treeshrink/R_scripts/plot_pergene.R
metaphlan/utils/treeshrink/R_scripts/plot_perspecies.R
metaphlan/utils/treeshrink/R_scripts/plot_threshold.R
metaphlan/utils/treeshrink/Rlib/BMS/CITATION
metaphlan/utils/treeshrink/Rlib/BMS/DESCRIPTION
metaphlan/utils/treeshrink/Rlib/BMS/INDEX
metaphlan/utils/treeshrink/Rlib/BMS/NAMESPACE
metaphlan/utils/treeshrink/Rlib/BMS/Meta/Rd.rds
metaphlan/utils/treeshrink/Rlib/BMS/Meta/data.rds
metaphlan/utils/treeshrink/Rlib/BMS/Meta/demo.rds
metaphlan/utils/treeshrink/Rlib/BMS/Meta/features.rds
metaphlan/utils/treeshrink/Rlib/BMS/Meta/hsearch.rds
metaphlan/utils/treeshrink/Rlib/BMS/Meta/links.rds
metaphlan/utils/treeshrink/Rlib/BMS/Meta/nsInfo.rds
metaphlan/utils/treeshrink/Rlib/BMS/Meta/package.rds
metaphlan/utils/treeshrink/Rlib/BMS/Meta/vignette.rds
metaphlan/utils/treeshrink/Rlib/BMS/R/BMS
metaphlan/utils/treeshrink/Rlib/BMS/R/BMS.rdb
metaphlan/utils/treeshrink/Rlib/BMS/R/BMS.rdx
metaphlan/utils/treeshrink/Rlib/BMS/data/datafls.rda
metaphlan/utils/treeshrink/Rlib/BMS/demo/BMS.growth.R
metaphlan/utils/treeshrink/Rlib/BMS/doc/bmasmall.bib
metaphlan/utils/treeshrink/Rlib/BMS/doc/bms.R
metaphlan/utils/treeshrink/Rlib/BMS/doc/bms.Rnw
metaphlan/utils/treeshrink/Rlib/BMS/doc/bms.pdf
metaphlan/utils/treeshrink/Rlib/BMS/doc/index.html
metaphlan/utils/treeshrink/Rlib/BMS/help/AnIndex
metaphlan/utils/treeshrink/Rlib/BMS/help/BMS.rdb
metaphlan/utils/treeshrink/Rlib/BMS/help/BMS.rdx
metaphlan/utils/treeshrink/Rlib/BMS/help/aliases.rds
metaphlan/utils/treeshrink/Rlib/BMS/help/paths.rds
metaphlan/utils/treeshrink/Rlib/BMS/html/00Index.html
metaphlan/utils/treeshrink/Rlib/BMS/html/R.css
metaphlan/utils/treeshrink/scripts/Tree_extend.py
metaphlan/utils/treeshrink/scripts/__init__.py
metaphlan/utils/treeshrink/scripts/alignment.py
metaphlan/utils/treeshrink/scripts/decompose_lib.py
metaphlan/utils/treeshrink/scripts/filemgr.py
metaphlan/utils/treeshrink/scripts/filter_lib.py
metaphlan/utils/treeshrink/scripts/optimal_filter_lib.py
metaphlan/utils/treeshrink/scripts/sequence_lib.py
metaphlan/utils/treeshrink/scripts/tree_lib.py
metaphlan/utils/treeshrink/scripts/util_lib.py