├── LICENSE ├── README.md ├── check_requirements.py ├── codetta.py ├── codetta_align.py ├── codetta_download.py ├── codetta_infer.py ├── codetta_summary.py ├── examples ├── GCA_014211875.1.fna ├── NC_013935.1.fna └── mito-db │ ├── metazoan_mito_ATP6.msa │ ├── metazoan_mito_ATP8.msa │ ├── metazoan_mito_COX1.msa │ ├── metazoan_mito_COX2.msa │ ├── metazoan_mito_COX3.msa │ ├── metazoan_mito_CYTB.msa │ ├── metazoan_mito_ND1.msa │ ├── metazoan_mito_ND2.msa │ ├── metazoan_mito_ND3.msa │ ├── metazoan_mito_ND4.msa │ ├── metazoan_mito_ND4L.msa │ ├── metazoan_mito_ND5.msa │ └── metazoan_mito_ND6.msa ├── helper_functions.py ├── hmmer.tar.gz ├── resources ├── bad_pfams.txt ├── mito_pfams.txt ├── pyrrolysine_pfams.txt ├── selenocysteine_pfams.txt ├── template_jobarray.sh ├── transposon_pfams.txt └── viral_pfams.txt └── setup.sh /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kshulgina/codetta/HEAD/LICENSE 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