├── .DS_Store ├── .gitignore ├── .travis.yml ├── KEGGDecoder ├── .DS_Store ├── .gitignore ├── Amphibactin │ ├── ABO2092homolog_ref.faa │ ├── ABO2093homolog_ref.faa │ ├── amphibactin.sfam.hmm │ ├── amphibactin2092_sfam_match.tblout │ └── amphibactin2093_sfam_match.tblout ├── DMSPLyase │ ├── .DS_Store │ ├── 14591.hmm │ ├── 25993.hmm │ ├── 274874.hmm │ ├── 94923.hmm │ ├── Pelagibacter_ref_dddK.faa │ └── dmdA_37326.hmm ├── DMSPSynthase │ ├── 4254.hmm │ ├── curson_dmsp_synthase.faa │ ├── img_dmsp_synthase_dsyB.faa │ └── ncbi_dmsp_synthase_dsyB.faa ├── Decode_and_Expand.py ├── DesferrioxamineBiosynthesis │ ├── Streptomycetes_ref_pathway.faa │ ├── ferrioxamine.sfam.hmm │ └── ferrioxamine_sfam_match.tblout ├── HMM_Models │ ├── .DS_Store │ ├── 14591.hmm │ ├── 25993.hmm │ ├── 274874.hmm │ ├── 4254.hmm │ ├── 94923.hmm │ ├── Ammonium_transp.hmm │ ├── AnfG_VnfG.hmm │ ├── Bac_rhodopsin.hmm │ ├── CbtB.hmm │ ├── Copper_HMA.hmm │ ├── DMSP_lyase.hmm │ ├── DsrD.hmm │ ├── Oxidored_nitro.hmm │ ├── PreviousExpanderDB_versions │ │ ├── Aminotran_5.hmm │ │ ├── PPC.hmm │ │ ├── PepSY.hmm │ │ ├── Peptidase_A8.hmm │ │ ├── Peptidase_C11.hmm │ │ ├── Peptidase_C25.hmm │ │ ├── Peptidase_M1.hmm │ │ ├── Peptidase_M14.hmm │ │ ├── Peptidase_M20.hmm │ │ ├── Peptidase_M24.hmm │ │ ├── Peptidase_M28.hmm │ │ ├── Peptidase_M29.hmm │ │ ├── Peptidase_M3.hmm │ │ ├── Peptidase_M50.hmm │ │ ├── Peptidase_M55.hmm │ │ ├── Peptidase_M61.hmm │ │ ├── Peptidase_S24.hmm │ │ ├── Peptidase_S26.hmm │ │ ├── expander_dbv0.1.hmm │ │ ├── expander_dbv0.2.hmm │ │ ├── expander_dbv0.3.hmm │ │ ├── expander_dbv0.4.hmm │ │ ├── expander_dbv0.5.hmm │ │ └── expander_dbv0.6.hmm │ ├── ZupT.hmm │ ├── amphibactin.sfam.hmm │ ├── anfD_nitrogenase.hmm │ ├── anfG_nitrogenase.hmm │ ├── anfK_nitrogenase.hmm │ ├── blh_betacarotenemonox.hmm │ ├── expander_dbv0.7.hmm │ ├── ferrioxamine.sfam.hmm │ ├── methylphosphonate-synthase.sfam.hmm │ ├── vnfD_nitrogenase.hmm │ ├── vnfG_nitrogenase.hmm │ └── vnfK_nitrogenase.hmm ├── KEGG_clustering.py ├── KEGG_clustering.pyc ├── KEGG_decoder.py ├── KEGG_expander.py ├── KOALA_definitions.txt ├── MakeTanglegram.py ├── MethylphosphonateSynthase │ ├── methylphosphonate-synthase.sfam.hmm │ ├── methylphosphonate-synthase_ref.faa │ └── methylphosphonate-synthase_sfam_match.tblout ├── Pfam_definitions.txt ├── Plotly_viz.py ├── PreviousKEGGDecoderVersions │ ├── Decode_and_Expand-V0.0.py │ ├── KEGG-decoderV0.3.py │ ├── KEGG-decoderV0.4.py │ ├── KEGG-decoderV0.5.py │ ├── KEGG-expanderV0.3.py │ ├── KEGG-expanderV0.4.1.py │ └── KOALA_definitionsV0.5.txt ├── README.md ├── __init__.py └── images │ ├── interactive.png │ ├── static.png │ └── tanglegram.png ├── LICENSE ├── README.md ├── pyproject.toml ├── tests ├── NORP_subset.txt ├── PET-function-test-ghostkoalaoutput.txt └── test_decoder.py └── tox.ini /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bjtully/BioData/HEAD/.DS_Store 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