├── .gitignore ├── LICENSE ├── README.md ├── data ├── 11427_2021_2081_MOESM1_ESM.pdf └── s11427-021-2081-6.pdf ├── scripts ├── Iteration.py ├── batch.py ├── genome2or.py └── src │ ├── CodeMessages.py │ ├── Functions.py │ ├── ParseArgs.py │ ├── __init__.py │ ├── __pycache__ │ ├── CodeMessages.cpython-36.pyc │ ├── CodeMessages.cpython-37.pyc │ ├── Functions.cpython-36.pyc │ ├── Functions.cpython-37.pyc │ ├── ParseArgs.cpython-36.pyc │ ├── ParseArgs.cpython-37.pyc │ ├── __init__.cpython-36.pyc │ ├── __init__.cpython-37.pyc │ ├── config.cpython-36.pyc │ └── config.cpython-37.pyc │ ├── config.py │ ├── data │ ├── Actinopteri.py │ ├── Amphibia.py │ ├── Aves.py │ ├── Branchiostoma_floridae.py │ ├── Chondrichthyes.py │ ├── Cladistia.py │ ├── Coelacanthimorpha.py │ ├── Crocodylia.py │ ├── Hyperoartia.py │ ├── Lepidosauria.py │ ├── Mammalia.py │ ├── Myxini.py │ ├── Reptiles.py │ ├── Testudines.py │ └── data.py │ ├── main.py │ └── test.py └── template ├── template.fas └── template.fasta 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