├── .gitignore ├── .pylintrc ├── .readthedocs.yaml ├── CHANGELOG.rst ├── LICENSE.txt ├── README.md ├── Snakefile ├── config_example.yaml ├── config_example2.yaml ├── config_example2_lorelei.yaml ├── data ├── example │ ├── ali.fa.gz │ ├── correct_only_genelist.txt │ ├── forest.nhx │ ├── genes │ │ ├── genes.Amia.calva.bed │ │ ├── genes.Astyanax.mexicanus.bed │ │ ├── genes.Danio.rerio.bed │ │ ├── genes.Esox.lucius.bed │ │ ├── genes.Gasterosteus.aculeatus.bed │ │ ├── genes.Lepisosteus.oculatus.bed │ │ ├── genes.Oncorhynchus.mykiss.bed │ │ ├── genes.Oreochromis.niloticus.bed │ │ ├── genes.Oryzias.latipes.bed │ │ ├── genes.Poecilia.formosa.bed │ │ ├── genes.Salmo.salar.bed │ │ ├── genes.Salvelinus.alpinus.bed │ │ ├── genes.Takifugu.rubripes.bed │ │ ├── genes.Tetraodon.nigroviridis.bed │ │ └── genes.Xiphophorus.maculatus.bed │ ├── genes_sp_mapping.txt │ ├── lowcov │ └── species_tree.nwk └── example2 │ ├── ali.fa.gz │ ├── genes │ ├── genes.Amia.calva.list │ ├── genes.Arapaima.gigas.list │ ├── genes.Danio.rerio.list │ ├── genes.Gasterosteus.aculeatus.list │ ├── genes.Lepisosteus.oculatus.list │ ├── genes.Oryzias.latipes.list │ ├── genes.Paramormyrops.kingsleyae.list │ └── genes.Scleropages.formosus.list │ ├── preduplication_ancgenes.tsv │ ├── species_tree.nwk │ └── trees.nhx ├── doc ├── Makefile ├── _static │ ├── Metropolis-Medium.otf │ └── style.css ├── conf.py ├── getting_started_installation.rst ├── getting_started_usage.rst ├── img │ ├── basic_sptree.png │ ├── diagnostic_by_homeo_bowfin.png │ ├── diagnostic_on_medaka.png │ ├── example_cor_27.png │ ├── example_ori_27.png │ ├── lore_on_medaka.png │ ├── scorpios_illustrated.png │ └── sptree_lore.png ├── index.rst ├── input_building_a_dataset.rst ├── input_description.rst ├── input_formatting.rst ├── input_your_configuration_file.rst ├── lorelei_configuration_file.rst ├── lorelei_introduction.rst ├── lorelei_usage.rst ├── make.bat ├── output_advanced.rst ├── output_genetrees.rst ├── output_treeviz.rst ├── project_changelog.rst ├── project_info.rst ├── requirements.txt ├── scripts.graphs.rst ├── scripts.lorelei.rst ├── scripts.rst ├── scripts.synteny.rst └── scripts.trees.rst ├── envs ├── graphs.yaml ├── plots.yaml ├── polytomysolver.yaml ├── rideogram.yaml └── scorpios.yaml ├── iterate_scorpios.sh ├── module_build_trees.smk ├── module_correct_trees.smk ├── module_graphs_orthogroups.smk ├── module_lorelei_diagnostic.smk ├── module_lorelei_lktests.smk ├── module_orthology_table.smk ├── module_synteny_ortho_para.smk ├── scorpios_lorelei.smk └── scripts ├── __init__.py ├── correct_subtrees_treebest.sh ├── graphs ├── __init__.py ├── combine_outgroups.py └── orthogroups.py ├── lorelei ├── __init__.py ├── constrained_aore_lore_topologies.py ├── fix_rideogram.py ├── homeologs_pairs_from_ancestor.py ├── homeologs_tree_conflicts.py ├── make_rideograms_inputs.py ├── plot_genome.R └── write_ancgenes_treeclass.py ├── make_lk_test_consel.sh ├── prototype_au_test3.sh ├── synteny ├── __init__.py ├── duplicated_families.py ├── f1_score_optimization.py ├── filter_no_synteny_genes.py ├── filter_regions.py ├── missed_orthologies.py ├── mygenome.py ├── pairwise_orthology_synteny.py ├── syntenycompare.py └── utilities.py └── trees ├── __init__.py ├── build_treebest_trees.py ├── convert_ids.py ├── cut_subtrees.py ├── genetree.py ├── inconsistent_trees.py ├── iteration_nhx_tags.py ├── make_tree_images.py ├── merge_subtrees.py ├── orthologs.py ├── parse_au_test.py ├── regraft_subtrees.py ├── speciestree.py └── utilities.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/.gitignore -------------------------------------------------------------------------------- /.pylintrc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/.pylintrc -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /CHANGELOG.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/CHANGELOG.rst -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/README.md -------------------------------------------------------------------------------- /Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/Snakefile -------------------------------------------------------------------------------- /config_example.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/config_example.yaml -------------------------------------------------------------------------------- /config_example2.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/config_example2.yaml -------------------------------------------------------------------------------- /config_example2_lorelei.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/config_example2_lorelei.yaml -------------------------------------------------------------------------------- /data/example/ali.fa.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/ali.fa.gz -------------------------------------------------------------------------------- /data/example/correct_only_genelist.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/correct_only_genelist.txt -------------------------------------------------------------------------------- /data/example/forest.nhx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/forest.nhx -------------------------------------------------------------------------------- /data/example/genes/genes.Amia.calva.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/genes/genes.Amia.calva.bed -------------------------------------------------------------------------------- /data/example/genes/genes.Astyanax.mexicanus.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/genes/genes.Astyanax.mexicanus.bed -------------------------------------------------------------------------------- /data/example/genes/genes.Danio.rerio.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/genes/genes.Danio.rerio.bed -------------------------------------------------------------------------------- /data/example/genes/genes.Esox.lucius.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/genes/genes.Esox.lucius.bed -------------------------------------------------------------------------------- /data/example/genes/genes.Gasterosteus.aculeatus.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/genes/genes.Gasterosteus.aculeatus.bed -------------------------------------------------------------------------------- /data/example/genes/genes.Lepisosteus.oculatus.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/genes/genes.Lepisosteus.oculatus.bed -------------------------------------------------------------------------------- /data/example/genes/genes.Oncorhynchus.mykiss.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/genes/genes.Oncorhynchus.mykiss.bed -------------------------------------------------------------------------------- /data/example/genes/genes.Oreochromis.niloticus.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/genes/genes.Oreochromis.niloticus.bed -------------------------------------------------------------------------------- /data/example/genes/genes.Oryzias.latipes.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/genes/genes.Oryzias.latipes.bed -------------------------------------------------------------------------------- /data/example/genes/genes.Poecilia.formosa.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/genes/genes.Poecilia.formosa.bed -------------------------------------------------------------------------------- /data/example/genes/genes.Salmo.salar.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/genes/genes.Salmo.salar.bed -------------------------------------------------------------------------------- /data/example/genes/genes.Salvelinus.alpinus.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/genes/genes.Salvelinus.alpinus.bed -------------------------------------------------------------------------------- /data/example/genes/genes.Takifugu.rubripes.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/genes/genes.Takifugu.rubripes.bed -------------------------------------------------------------------------------- /data/example/genes/genes.Tetraodon.nigroviridis.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/genes/genes.Tetraodon.nigroviridis.bed -------------------------------------------------------------------------------- /data/example/genes/genes.Xiphophorus.maculatus.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/genes/genes.Xiphophorus.maculatus.bed -------------------------------------------------------------------------------- /data/example/genes_sp_mapping.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/genes_sp_mapping.txt -------------------------------------------------------------------------------- /data/example/lowcov: -------------------------------------------------------------------------------- 1 | Xiphophorus.maculatus 2 | -------------------------------------------------------------------------------- /data/example/species_tree.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example/species_tree.nwk -------------------------------------------------------------------------------- /data/example2/ali.fa.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example2/ali.fa.gz -------------------------------------------------------------------------------- /data/example2/genes/genes.Amia.calva.list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example2/genes/genes.Amia.calva.list -------------------------------------------------------------------------------- /data/example2/genes/genes.Arapaima.gigas.list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example2/genes/genes.Arapaima.gigas.list -------------------------------------------------------------------------------- /data/example2/genes/genes.Danio.rerio.list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example2/genes/genes.Danio.rerio.list -------------------------------------------------------------------------------- /data/example2/genes/genes.Gasterosteus.aculeatus.list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example2/genes/genes.Gasterosteus.aculeatus.list -------------------------------------------------------------------------------- /data/example2/genes/genes.Lepisosteus.oculatus.list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example2/genes/genes.Lepisosteus.oculatus.list -------------------------------------------------------------------------------- /data/example2/genes/genes.Oryzias.latipes.list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example2/genes/genes.Oryzias.latipes.list -------------------------------------------------------------------------------- /data/example2/genes/genes.Paramormyrops.kingsleyae.list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example2/genes/genes.Paramormyrops.kingsleyae.list -------------------------------------------------------------------------------- /data/example2/genes/genes.Scleropages.formosus.list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example2/genes/genes.Scleropages.formosus.list -------------------------------------------------------------------------------- /data/example2/preduplication_ancgenes.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example2/preduplication_ancgenes.tsv -------------------------------------------------------------------------------- /data/example2/species_tree.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example2/species_tree.nwk -------------------------------------------------------------------------------- /data/example2/trees.nhx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/data/example2/trees.nhx -------------------------------------------------------------------------------- /doc/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/Makefile -------------------------------------------------------------------------------- /doc/_static/Metropolis-Medium.otf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/_static/Metropolis-Medium.otf -------------------------------------------------------------------------------- /doc/_static/style.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/_static/style.css -------------------------------------------------------------------------------- /doc/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/conf.py -------------------------------------------------------------------------------- /doc/getting_started_installation.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/getting_started_installation.rst -------------------------------------------------------------------------------- /doc/getting_started_usage.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/getting_started_usage.rst -------------------------------------------------------------------------------- /doc/img/basic_sptree.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/img/basic_sptree.png -------------------------------------------------------------------------------- /doc/img/diagnostic_by_homeo_bowfin.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/img/diagnostic_by_homeo_bowfin.png -------------------------------------------------------------------------------- /doc/img/diagnostic_on_medaka.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/img/diagnostic_on_medaka.png -------------------------------------------------------------------------------- /doc/img/example_cor_27.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/img/example_cor_27.png -------------------------------------------------------------------------------- /doc/img/example_ori_27.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/img/example_ori_27.png -------------------------------------------------------------------------------- /doc/img/lore_on_medaka.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/img/lore_on_medaka.png -------------------------------------------------------------------------------- /doc/img/scorpios_illustrated.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/img/scorpios_illustrated.png -------------------------------------------------------------------------------- /doc/img/sptree_lore.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/img/sptree_lore.png -------------------------------------------------------------------------------- /doc/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/index.rst -------------------------------------------------------------------------------- /doc/input_building_a_dataset.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/input_building_a_dataset.rst -------------------------------------------------------------------------------- /doc/input_description.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/input_description.rst -------------------------------------------------------------------------------- /doc/input_formatting.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/input_formatting.rst -------------------------------------------------------------------------------- /doc/input_your_configuration_file.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/input_your_configuration_file.rst -------------------------------------------------------------------------------- /doc/lorelei_configuration_file.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/lorelei_configuration_file.rst -------------------------------------------------------------------------------- /doc/lorelei_introduction.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/lorelei_introduction.rst -------------------------------------------------------------------------------- /doc/lorelei_usage.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/lorelei_usage.rst -------------------------------------------------------------------------------- /doc/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/make.bat -------------------------------------------------------------------------------- /doc/output_advanced.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/output_advanced.rst -------------------------------------------------------------------------------- /doc/output_genetrees.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/output_genetrees.rst -------------------------------------------------------------------------------- /doc/output_treeviz.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/output_treeviz.rst -------------------------------------------------------------------------------- /doc/project_changelog.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/project_changelog.rst -------------------------------------------------------------------------------- /doc/project_info.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/project_info.rst -------------------------------------------------------------------------------- /doc/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/requirements.txt -------------------------------------------------------------------------------- /doc/scripts.graphs.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/scripts.graphs.rst -------------------------------------------------------------------------------- /doc/scripts.lorelei.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/scripts.lorelei.rst -------------------------------------------------------------------------------- /doc/scripts.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/scripts.rst -------------------------------------------------------------------------------- /doc/scripts.synteny.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/scripts.synteny.rst -------------------------------------------------------------------------------- /doc/scripts.trees.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/doc/scripts.trees.rst -------------------------------------------------------------------------------- /envs/graphs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/envs/graphs.yaml -------------------------------------------------------------------------------- /envs/plots.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/envs/plots.yaml -------------------------------------------------------------------------------- /envs/polytomysolver.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/envs/polytomysolver.yaml -------------------------------------------------------------------------------- /envs/rideogram.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/envs/rideogram.yaml -------------------------------------------------------------------------------- /envs/scorpios.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/envs/scorpios.yaml -------------------------------------------------------------------------------- /iterate_scorpios.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/iterate_scorpios.sh -------------------------------------------------------------------------------- /module_build_trees.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/module_build_trees.smk -------------------------------------------------------------------------------- /module_correct_trees.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/module_correct_trees.smk -------------------------------------------------------------------------------- /module_graphs_orthogroups.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/module_graphs_orthogroups.smk -------------------------------------------------------------------------------- /module_lorelei_diagnostic.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/module_lorelei_diagnostic.smk -------------------------------------------------------------------------------- /module_lorelei_lktests.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/module_lorelei_lktests.smk -------------------------------------------------------------------------------- /module_orthology_table.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/module_orthology_table.smk -------------------------------------------------------------------------------- /module_synteny_ortho_para.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/module_synteny_ortho_para.smk -------------------------------------------------------------------------------- /scorpios_lorelei.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scorpios_lorelei.smk -------------------------------------------------------------------------------- /scripts/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scripts/correct_subtrees_treebest.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/correct_subtrees_treebest.sh -------------------------------------------------------------------------------- /scripts/graphs/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scripts/graphs/combine_outgroups.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/graphs/combine_outgroups.py -------------------------------------------------------------------------------- /scripts/graphs/orthogroups.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/graphs/orthogroups.py -------------------------------------------------------------------------------- /scripts/lorelei/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scripts/lorelei/constrained_aore_lore_topologies.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/lorelei/constrained_aore_lore_topologies.py -------------------------------------------------------------------------------- /scripts/lorelei/fix_rideogram.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/lorelei/fix_rideogram.py -------------------------------------------------------------------------------- /scripts/lorelei/homeologs_pairs_from_ancestor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/lorelei/homeologs_pairs_from_ancestor.py -------------------------------------------------------------------------------- /scripts/lorelei/homeologs_tree_conflicts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/lorelei/homeologs_tree_conflicts.py -------------------------------------------------------------------------------- /scripts/lorelei/make_rideograms_inputs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/lorelei/make_rideograms_inputs.py -------------------------------------------------------------------------------- /scripts/lorelei/plot_genome.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/lorelei/plot_genome.R -------------------------------------------------------------------------------- /scripts/lorelei/write_ancgenes_treeclass.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/lorelei/write_ancgenes_treeclass.py -------------------------------------------------------------------------------- /scripts/make_lk_test_consel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/make_lk_test_consel.sh -------------------------------------------------------------------------------- /scripts/prototype_au_test3.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/prototype_au_test3.sh -------------------------------------------------------------------------------- /scripts/synteny/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scripts/synteny/duplicated_families.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/synteny/duplicated_families.py -------------------------------------------------------------------------------- /scripts/synteny/f1_score_optimization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/synteny/f1_score_optimization.py -------------------------------------------------------------------------------- /scripts/synteny/filter_no_synteny_genes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/synteny/filter_no_synteny_genes.py -------------------------------------------------------------------------------- /scripts/synteny/filter_regions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/synteny/filter_regions.py -------------------------------------------------------------------------------- /scripts/synteny/missed_orthologies.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/synteny/missed_orthologies.py -------------------------------------------------------------------------------- /scripts/synteny/mygenome.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/synteny/mygenome.py -------------------------------------------------------------------------------- /scripts/synteny/pairwise_orthology_synteny.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/synteny/pairwise_orthology_synteny.py -------------------------------------------------------------------------------- /scripts/synteny/syntenycompare.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/synteny/syntenycompare.py -------------------------------------------------------------------------------- /scripts/synteny/utilities.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/synteny/utilities.py -------------------------------------------------------------------------------- /scripts/trees/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scripts/trees/build_treebest_trees.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/trees/build_treebest_trees.py -------------------------------------------------------------------------------- /scripts/trees/convert_ids.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/trees/convert_ids.py -------------------------------------------------------------------------------- /scripts/trees/cut_subtrees.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/trees/cut_subtrees.py -------------------------------------------------------------------------------- /scripts/trees/genetree.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/trees/genetree.py -------------------------------------------------------------------------------- /scripts/trees/inconsistent_trees.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/trees/inconsistent_trees.py -------------------------------------------------------------------------------- /scripts/trees/iteration_nhx_tags.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/trees/iteration_nhx_tags.py -------------------------------------------------------------------------------- /scripts/trees/make_tree_images.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/trees/make_tree_images.py -------------------------------------------------------------------------------- /scripts/trees/merge_subtrees.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/trees/merge_subtrees.py -------------------------------------------------------------------------------- /scripts/trees/orthologs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/trees/orthologs.py -------------------------------------------------------------------------------- /scripts/trees/parse_au_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/trees/parse_au_test.py -------------------------------------------------------------------------------- /scripts/trees/regraft_subtrees.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/trees/regraft_subtrees.py -------------------------------------------------------------------------------- /scripts/trees/speciestree.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/trees/speciestree.py -------------------------------------------------------------------------------- /scripts/trees/utilities.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DyogenIBENS/SCORPIOS/HEAD/scripts/trees/utilities.py --------------------------------------------------------------------------------