├── .github └── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── README.html ├── README.md ├── README_files ├── a.html ├── example-plot-good.png ├── example-plot-poor.png ├── frameworks-41c2037bf12f1e46d8f08b88a04a8d8f.css ├── frameworks-a3b8a10d4a9e37a78f033ef4a4f525f5.css ├── github-a842d1324eb4ab086590be512b951c4c.css ├── github-e3bff23d54e12a76d66b61023f1c8796.css ├── octicons.css ├── progress-bar.png ├── site-294181adec18ed639e160b96b45d17ac.css ├── site-bdd55e67f0ed3e8974c7c941589e8c6a.css └── status.svg ├── TODO.md ├── examples ├── config_example.conf ├── test_aln_aa.fasta ├── test_aln_nt.fasta └── test_guide_cladogram.newick ├── paper.aux ├── paper.bib ├── paper.md ├── setup.py ├── spruceup-fig1.png ├── spruceup ├── __init__.py ├── __main__.py ├── aln_parsing.py ├── aln_writing.py └── spruceup.py └── tests ├── __init__.py ├── metamorphic_tests ├── __init__.py ├── complement.py ├── 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