├── .gitignore ├── LICENSE ├── README.md ├── _example_files ├── blosum50.matrix └── parameter_file ├── _scripts ├── 1_3_addTruePseudogenes2.py ├── 1_3_annotatePseudogenes.py ├── 1_3_filterOutPseuRMs.py ├── 1_3_getPseudoGFF.py ├── 1_3_pseuOrigToTrue.py ├── 1_3_removeCodeNamesFromRM4col.py ├── 1_3_v2_MakeFastaCodeName.py ├── 1_3_v2_verifyPseudogenes.py ├── BlastUtility.py ├── FastaManager.py ├── FileUtility.py ├── GFFUtil.py ├── ParseBlast.py ├── PseudogenePipeline.py ├── Seq_GFFtoIntron4col_v2.py ├── Seq_removeGFFaltSplicing.py ├── SingleLinkage.py ├── TabularManager.py ├── Translation.py ├── TruncateGeneNames.py ├── __pycache__ │ ├── BlastUtility.cpython-39.pyc │ ├── FastaManager.cpython-39.pyc │ ├── FileUtility.cpython-39.pyc │ ├── ParseBlast.cpython-39.pyc │ ├── SingleLinkage.cpython-39.pyc │ └── Translation.cpython-39.pyc ├── parse_RepeatMasker_gff.py ├── script_just25.py ├── script_step2e.py ├── script_step3.5.py ├── script_step3bDave.py ├── script_step6.py └── 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