├── .github └── ISSUE_TEMPLATE │ └── bug_report.md ├── .gitignore ├── BAD_Mutations.py ├── CHANGELOG.md ├── CONTRIBUTING.md ├── LICENSE ├── Manual ├── Installation.md ├── Manual_v1.0.md ├── Manual_v1.0.txt ├── alignment.png └── del_tol.png ├── Manuscript_Scripts ├── README.md ├── additional_1000genes │ ├── README.md │ ├── input │ │ ├── fasta.list00 │ │ ├── fasta.list01 │ │ ├── rest │ │ ├── rest_sub.list │ │ ├── sorted_MSA.list00 │ │ ├── sorted_MSA.list01 │ │ ├── sorted_fasta_tree.list00 │ │ ├── sorted_fasta_tree.list01 │ │ ├── sorted_sub.list01 │ │ ├── sorted_sub_tree.list00 │ │ ├── sorted_tree.list00 │ │ └── sorted_tree.list01 │ ├── jobs │ │ ├── run_alignment_list00.job │ │ ├── run_alignment_list01.job │ │ ├── run_prediction_mesabi00.job │ │ └── run_prediction_mesabi01.job │ ├── output │ │ └── sorted_973_Combined_Report.txt │ └── script │ │ ├── creat_annova.pl │ │ └── extract_prediction.sh ├── jobs │ ├── run_align_predict.job │ └── run_prediction.job └── script │ ├── creat_subs_file.sh │ ├── ensemble.R │ ├── extract_prediction.sh │ ├── extract_target_fasta.py │ ├── fasta_splitter.pl │ ├── filtering_prediction.pl │ └── get_unpredicted_gene.pl ├── README.md ├── Sample_Config.txt ├── Shell_Scripts ├── Clustalo_Align.sh ├── LRT.hyphy ├── Pasta_Align.sh ├── Prank_Align.sh ├── Prediction.sh ├── Prepare_HyPhy.sh ├── Seq_From_BLASTdb.sh ├── Unzip_CDS.sh └── get_dependencies.sh ├── Supporting ├── VeP_to_Subs.py └── bad_mutations.yml ├── Test_Data ├── ADH3.fasta ├── ADH3.subs ├── CBF3.fasta ├── CBF3.subs ├── Faldh.fasta ├── Faldh.subs ├── G3PDH.fasta ├── G3PDH.subs ├── MSA │ ├── ADH3_MSA.fasta │ ├── CBF3_MSA.fasta │ ├── Faldh_MSA.fasta │ ├── G3PDH_MSA.fasta │ ├── PEPC_MSA.fasta │ └── STK_MSA.fasta ├── PEPC.fasta ├── PEPC.subs ├── Reports │ ├── ADH3_Predictions.txt │ ├── CBF3_Predictions.txt │ ├── Combined_Report.txt │ ├── Faldh_Predictions.txt │ ├── G3PDH_Predictions.txt │ ├── PEPC_Predictions.txt │ └── STK_Predictions.txt ├── STK.fasta ├── STK.subs └── Tree │ ├── ADH3.tree │ ├── CBF3.tree │ ├── Faldh.tree │ ├── G3PDH.tree │ ├── PEPC.tree │ └── STK.tree └── lrt_predict ├── Blast ├── __init__.py ├── blast_search.py └── sequence_fetch.py ├── Fetch ├── __init__.py ├── ensembl.py ├── ensembl_species.py ├── fetch.py ├── format_blast.py ├── phytozome.py └── phytozome_species.py ├── General ├── __init__.py ├── check_args.py ├── check_modules.py ├── dir_funcs.py ├── file_funcs.py ├── parse_args.py ├── parse_input.py └── set_verbosity.py ├── Predict ├── __init__.py ├── align.py ├── hyphy_parser.py └── predict.py ├── Setup ├── __init__.py ├── parse_config.py └── setup_env.py └── __init__.py /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MorrellLAB/BAD_Mutations/HEAD/.github/ISSUE_TEMPLATE/bug_report.md -------------------------------------------------------------------------------- /.gitignore: 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