├── .gitignore ├── Dockerfile ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── docs ├── CaseStudy │ ├── CFSAN000189-chrom.fasta │ ├── Sbareilly-10taxon.tre │ └── outputFilesForManuscript │ │ ├── snpma_15X.fasta │ │ ├── snpma_1X-NOSNPs-FOUND │ │ ├── snpma_30X.fasta │ │ └── snpma_5X.fasta ├── TTR-figure.pdf ├── TTR-figure.png ├── TTR_preprint.tex ├── TTR_submission.tex ├── note.bib ├── note.tex └── tutorial.md ├── environment.yml ├── example.config ├── example ├── ErrprofR1.txt ├── ErrprofR2.txt ├── barref.fasta ├── example.tre ├── mini_ref.fasta └── simtree.tre ├── example_indels.config ├── run_tests.sh ├── setup.py ├── tests ├── check_refgenome.py ├── garli_mini.conf ├── input │ ├── alt.tre │ ├── mini_ref.fasta │ ├── mini_ref_multi.fasta │ ├── simple.cfg │ ├── simple.tre │ ├── simple_clustering.cfg │ ├── simple_expected.tre │ ├── test1.cfg │ ├── test2.cfg │ └── tree_from_fasta.cfg ├── integration_test.py ├── multi.config ├── multi_indel.config └── tree_from_fasta.py ├── treetoreads.py 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