├── .gitignore ├── LICENSE ├── README.md ├── azure-pipelines.yml ├── bin ├── .pylintrc ├── convert_distance_matrix_to_phylip.py ├── ntsynt_viz.py ├── ntsynt_viz.smk ├── ntsynt_viz_distance_cladogram.R ├── ntsynt_viz_find_plot_nudges.py ├── ntsynt_viz_format_blocks_gggenomes.py ├── ntsynt_viz_normalize_strands.py ├── ntsynt_viz_output_orders.py ├── ntsynt_viz_plot_synteny_blocks_ribbon_plot.R ├── ntsynt_viz_sort_sequences.py ├── ntsynt_viz_synteny_distance_estimation.py ├── rename_synteny_blocks.py └── sort_ntsynt_blocks.py ├── conversion_scripts ├── convert_halsynteny_to_ntsynt_blocks.py └── convert_syri_to_ntsynt_blocks.py ├── ntsynt-viz_logo_colors.png └── tests ├── GCA_000001405.15_GRCh38_genomic.chr-only.nums.fa.fai ├── GCA_021498465.1_ASM2149846v1_genomic.renamed.chr.fa.fai ├── GCF_002880755.1_Clint_PTRv2_genomic.chr-only.rename.fa.fai ├── GCF_008122165.1_Kamilah_GGO_v0_genomic.chr-only.rename.fa.fai ├── GCF_013052645.1_Mhudiblu_PPA_v0_genomic.chr-only.rename.fa.fai ├── GCF_028885625.2_NHGRI_mPonPyg2-v2.0_pri_genomic.chr.renamed.fa.fai ├── expected └── great-apes_ribbon-plots_no-tree_est-distances.order.tsv ├── fais.tsv ├── great-apes.mt-tree.nwk ├── great-apes.name-conversions.tsv ├── great-apes.ntSynt.synteny_blocks.tsv ├── great-apes_ribbon-plots.example1.png └── great-apes_ribbon-plots.example2.png /.gitignore: -------------------------------------------------------------------------------- 1 | .snakemake 2 | file_sources 3 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcgsc/ntSynt-viz/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcgsc/ntSynt-viz/HEAD/README.md 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