├── .github └── workflows │ ├── black.yml │ └── publish-to-pypi.yml ├── CITATION.cff ├── LICENSE ├── README.md ├── config ├── config.json └── hg002v1.1.cenSatv2.0.bed ├── images ├── Chr1:14000001-18000000_FULL.png ├── chr13_MATERNAL:1-4000000_TRI_ANNOTATED.png ├── chr13_MATERNAL:1-4000000_chr14_MATERNAL:1-4000000_COMPARE.png ├── chr14:2000000-5000000_chr21:2000000-5000000.png ├── chr1_screenshot.png ├── demo.gif ├── logo.png ├── moddotplot_comparative.png ├── moddotplot_output.png └── portforwarding.png ├── pyproject.toml ├── sequences ├── Arabadopsis_chr1_centromere.fa ├── hg002_chr13_MATERNAL:1-4000000.fa └── hg002_chr14_MATERNAL:1-4000000.fa └── src └── moddotplot ├── __init__.py ├── __main__.py ├── assets └── favicon.png ├── const.py ├── estimate_identity.py ├── interactive.py ├── moddotplot.py ├── parse_fasta.py └── static_plots.py /.github/workflows/black.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/.github/workflows/black.yml -------------------------------------------------------------------------------- /.github/workflows/publish-to-pypi.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/.github/workflows/publish-to-pypi.yml -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/CITATION.cff -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/README.md -------------------------------------------------------------------------------- /config/config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/config/config.json -------------------------------------------------------------------------------- /config/hg002v1.1.cenSatv2.0.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/config/hg002v1.1.cenSatv2.0.bed -------------------------------------------------------------------------------- /images/Chr1:14000001-18000000_FULL.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/images/Chr1:14000001-18000000_FULL.png -------------------------------------------------------------------------------- /images/chr13_MATERNAL:1-4000000_TRI_ANNOTATED.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/images/chr13_MATERNAL:1-4000000_TRI_ANNOTATED.png -------------------------------------------------------------------------------- /images/chr13_MATERNAL:1-4000000_chr14_MATERNAL:1-4000000_COMPARE.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/images/chr13_MATERNAL:1-4000000_chr14_MATERNAL:1-4000000_COMPARE.png -------------------------------------------------------------------------------- /images/chr14:2000000-5000000_chr21:2000000-5000000.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/images/chr14:2000000-5000000_chr21:2000000-5000000.png -------------------------------------------------------------------------------- /images/chr1_screenshot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/images/chr1_screenshot.png -------------------------------------------------------------------------------- /images/demo.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/images/demo.gif -------------------------------------------------------------------------------- /images/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/images/logo.png -------------------------------------------------------------------------------- /images/moddotplot_comparative.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/images/moddotplot_comparative.png -------------------------------------------------------------------------------- /images/moddotplot_output.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/images/moddotplot_output.png -------------------------------------------------------------------------------- /images/portforwarding.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/images/portforwarding.png -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/pyproject.toml -------------------------------------------------------------------------------- /sequences/Arabadopsis_chr1_centromere.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/sequences/Arabadopsis_chr1_centromere.fa -------------------------------------------------------------------------------- /sequences/hg002_chr13_MATERNAL:1-4000000.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/sequences/hg002_chr13_MATERNAL:1-4000000.fa -------------------------------------------------------------------------------- /sequences/hg002_chr14_MATERNAL:1-4000000.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/sequences/hg002_chr14_MATERNAL:1-4000000.fa -------------------------------------------------------------------------------- /src/moddotplot/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /src/moddotplot/__main__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/src/moddotplot/__main__.py -------------------------------------------------------------------------------- /src/moddotplot/assets/favicon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/src/moddotplot/assets/favicon.png -------------------------------------------------------------------------------- /src/moddotplot/const.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/src/moddotplot/const.py -------------------------------------------------------------------------------- /src/moddotplot/estimate_identity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/src/moddotplot/estimate_identity.py -------------------------------------------------------------------------------- /src/moddotplot/interactive.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/src/moddotplot/interactive.py -------------------------------------------------------------------------------- /src/moddotplot/moddotplot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/src/moddotplot/moddotplot.py -------------------------------------------------------------------------------- /src/moddotplot/parse_fasta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/src/moddotplot/parse_fasta.py -------------------------------------------------------------------------------- /src/moddotplot/static_plots.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marbl/ModDotPlot/HEAD/src/moddotplot/static_plots.py --------------------------------------------------------------------------------