├── .coveragerc ├── .coveralls.yml ├── .github └── workflows │ ├── build.yml │ └── docker.yml ├── .gitignore ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── README.md ├── conda └── meta.yaml ├── docs ├── calc.md ├── call.md ├── favicon.png ├── filter.md ├── geno.md ├── genome.md ├── hmm.md ├── hmm.sketch ├── hmm_example.png ├── hmm_opts.png ├── index.md ├── logo.png ├── logo.sketch ├── phylo.md ├── primer.md ├── rename.md ├── requirements.txt ├── tajima.md ├── tajima.png ├── tajima.sketch ├── vcf2sql.md └── vcf2tsv.md ├── mkdocs.yml ├── requirements.txt ├── setup.cfg ├── setup.py ├── test_data ├── DL238.ab1 ├── DL238.vcf.gz ├── DL238.vcf.gz.csi ├── QX1211.indels.vcf.gz ├── gatk.vcf ├── nucleotides.fasta ├── snpeff_test.vcf.gz └── test.vcf.gz ├── tests ├── __init__.py ├── test_calc.py ├── test_call.py ├── test_genome.py ├── test_phylo.py ├── test_primer.py ├── test_rename.py ├── test_tajima.py └── test_utilities.py └── vcfkit ├── __init__.py ├── annotate.py ├── calc.py ├── call.py ├── filter.py ├── geno.py ├── genome.py ├── hmm.py ├── phylo.py ├── primer.py ├── rename.py ├── stat.py ├── static ├── jquery-1.11.3.min.js ├── jsphylosvg-1.55 │ ├── jsphylosvg-min.js │ ├── jsphylosvg.js │ ├── raphael-min.js │ └── readme.txt ├── primer3_config │ ├── dangle.dh │ ├── dangle.ds │ ├── interpretations │ │ ├── dangle_i.dh │ │ ├── dangle_i.ds │ │ ├── loops_i.dh │ │ ├── loops_i.ds │ │ ├── stack_i.dh │ │ ├── stack_i.ds │ │ ├── stackmm_i_mm.dh │ │ ├── stackmm_i_mm.ds │ │ ├── tetraloop_i.dh │ │ ├── tetraloop_i.ds │ │ ├── triloop_i.dh │ │ ├── triloop_i.ds │ │ ├── tstack2_i.dh │ │ ├── tstack2_i.ds │ │ ├── tstack_i.dh │ │ ├── tstack_i.ds │ │ ├── tstack_tm_inf_i.dh │ │ └── tstack_tm_inf_i.ds │ ├── loops.dh │ ├── loops.ds │ ├── primer3.license.txt │ ├── stack.dh │ ├── stack.ds │ ├── stackmm.dh │ ├── stackmm.ds │ ├── tetraloop.dh │ ├── tetraloop.ds │ ├── triloop.dh │ ├── triloop.ds │ ├── tstack.dh │ ├── tstack2.dh │ ├── tstack2.ds │ └── tstack_tm_inf.ds └── tree.html ├── tajima.py ├── 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