├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md └── workflows │ └── ci.yml ├── .gitignore ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── README.md ├── examples ├── Albania │ ├── README.md │ ├── data │ │ ├── Albanian.tree.152tax.tre │ │ ├── copy_states.csv │ │ ├── data.txt │ │ ├── maps │ │ │ ├── Albanian_map_ACCTRAN.html │ │ │ ├── Albanian_map_ALL_EFT.html │ │ │ ├── Albanian_map_ALL_F81.html │ │ │ ├── Albanian_map_ALL_JC.html │ │ │ ├── Albanian_map_COPY.html │ │ │ ├── Albanian_map_DELTRAN.html │ │ │ ├── Albanian_map_DOWNPASS.html │ │ │ ├── Albanian_map_JOINT_EFT.html │ │ │ ├── Albanian_map_JOINT_F81.html │ │ │ ├── Albanian_map_JOINT_JC.html │ │ │ ├── Albanian_map_MAP_EFT.html │ │ │ ├── Albanian_map_MAP_F81.html │ │ │ ├── Albanian_map_MAP_JC.html │ │ │ ├── Albanian_map_ML_EFT.html │ │ │ ├── Albanian_map_ML_F81.html │ │ │ ├── Albanian_map_ML_JC.html │ │ │ ├── Albanian_map_MP.html │ │ │ ├── Albanian_map_MPPA_EFT.html │ │ │ ├── Albanian_map_MPPA_F81.html │ │ │ └── Albanian_map_MPPA_JC.html │ │ ├── pastml │ │ │ ├── ACCTRAN │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ └── params.character_Country.method_ACCTRAN.tab │ │ │ ├── ALL │ │ │ │ ├── EFT │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── iTOL_colorstrip-Country_ACCTRAN.txt │ │ │ │ │ ├── iTOL_colorstrip-Country_DELTRAN.txt │ │ │ │ │ ├── iTOL_colorstrip-Country_DOWNPASS.txt │ │ │ │ │ ├── iTOL_colorstrip-Country_JOINT.txt │ │ │ │ │ ├── iTOL_colorstrip-Country_MAP.txt │ │ │ │ │ ├── iTOL_colorstrip-Country_MPPA.txt │ │ │ │ │ ├── iTOL_popup_info.txt │ │ │ │ │ ├── iTOL_style-Country_ACCTRAN.txt │ │ │ │ │ ├── iTOL_style-Country_DELTRAN.txt │ │ │ │ │ ├── iTOL_style-Country_DOWNPASS.txt │ │ │ │ │ ├── iTOL_style-Country_JOINT.txt │ │ │ │ │ ├── iTOL_style-Country_MAP.txt │ │ │ │ │ ├── iTOL_style-Country_MPPA.txt │ │ │ │ │ ├── iTOL_tree_id.txt │ │ │ │ │ ├── iTOL_url.txt │ │ │ │ │ ├── marginal_probabilities.character_Country_MAP.model_EFT.tab │ │ │ │ │ ├── marginal_probabilities.character_Country_MPPA.model_EFT.tab │ │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ │ ├── params.character_Country_ACCTRAN.method_ACCTRAN.tab │ │ │ │ │ ├── params.character_Country_DELTRAN.method_DELTRAN.tab │ │ │ │ │ ├── params.character_Country_DOWNPASS.method_DOWNPASS.tab │ │ │ │ │ ├── params.character_Country_JOINT.method_JOINT.model_EFT.tab │ │ │ │ │ ├── params.character_Country_MAP.method_MAP.model_EFT.tab │ │ │ │ │ └── params.character_Country_MPPA.method_MPPA.model_EFT.tab │ │ │ │ ├── F81 │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── iTOL_colorstrip-Country_ACCTRAN.txt │ │ │ │ │ ├── iTOL_colorstrip-Country_DELTRAN.txt │ │ │ │ │ ├── iTOL_colorstrip-Country_DOWNPASS.txt │ │ │ │ │ ├── iTOL_colorstrip-Country_JOINT.txt │ │ │ │ │ ├── iTOL_colorstrip-Country_MAP.txt │ │ │ │ │ ├── iTOL_colorstrip-Country_MPPA.txt │ │ │ │ │ ├── iTOL_popup_info.txt │ │ │ │ │ ├── iTOL_style-Country_ACCTRAN.txt │ │ │ │ │ ├── iTOL_style-Country_DELTRAN.txt │ │ │ │ │ ├── iTOL_style-Country_DOWNPASS.txt │ │ │ │ │ ├── iTOL_style-Country_JOINT.txt │ │ │ │ │ ├── iTOL_style-Country_MAP.txt │ │ │ │ │ ├── iTOL_style-Country_MPPA.txt │ │ │ │ │ ├── iTOL_tree_id.txt │ │ │ │ │ ├── iTOL_url.txt │ │ │ │ │ ├── marginal_probabilities.character_Country_MAP.model_F81.tab │ │ │ │ │ ├── marginal_probabilities.character_Country_MPPA.model_F81.tab │ │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ │ ├── params.character_Country_ACCTRAN.method_ACCTRAN.tab │ │ │ │ │ ├── params.character_Country_DELTRAN.method_DELTRAN.tab │ │ │ │ │ ├── params.character_Country_DOWNPASS.method_DOWNPASS.tab │ │ │ │ │ ├── params.character_Country_JOINT.method_JOINT.model_F81.tab │ │ │ │ │ ├── params.character_Country_MAP.method_MAP.model_F81.tab │ │ │ │ │ └── params.character_Country_MPPA.method_MPPA.model_F81.tab │ │ │ │ └── JC │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── iTOL_colorstrip-Country_ACCTRAN.txt │ │ │ │ │ ├── iTOL_colorstrip-Country_DELTRAN.txt │ │ │ │ │ ├── iTOL_colorstrip-Country_DOWNPASS.txt │ │ │ │ │ ├── iTOL_colorstrip-Country_JOINT.txt │ │ │ │ │ ├── iTOL_colorstrip-Country_MAP.txt │ │ │ │ │ ├── iTOL_colorstrip-Country_MPPA.txt │ │ │ │ │ ├── iTOL_popup_info.txt │ │ │ │ │ ├── iTOL_style-Country_ACCTRAN.txt │ │ │ │ │ ├── iTOL_style-Country_DELTRAN.txt │ │ │ │ │ ├── iTOL_style-Country_DOWNPASS.txt │ │ │ │ │ ├── iTOL_style-Country_JOINT.txt │ │ │ │ │ ├── iTOL_style-Country_MAP.txt │ │ │ │ │ ├── iTOL_style-Country_MPPA.txt │ │ │ │ │ ├── iTOL_tree_id.txt │ │ │ │ │ ├── iTOL_url.txt │ │ │ │ │ ├── marginal_probabilities.character_Country_MAP.model_JC.tab │ │ │ │ │ ├── marginal_probabilities.character_Country_MPPA.model_JC.tab │ │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ │ ├── params.character_Country_ACCTRAN.method_ACCTRAN.tab │ │ │ │ │ ├── params.character_Country_DELTRAN.method_DELTRAN.tab │ │ │ │ │ ├── params.character_Country_DOWNPASS.method_DOWNPASS.tab │ │ │ │ │ ├── params.character_Country_JOINT.method_JOINT.model_JC.tab │ │ │ │ │ ├── params.character_Country_MAP.method_MAP.model_JC.tab │ │ │ │ │ └── params.character_Country_MPPA.method_MPPA.model_JC.tab │ │ │ ├── COPY │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ └── params.character_Country.method_COPY.tab │ │ │ ├── DELTRAN │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ └── params.character_Country.method_DELTRAN.tab │ │ │ ├── DOWNPASS │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ └── params.character_Country.method_DOWNPASS.tab │ │ │ ├── JOINT │ │ │ │ ├── EFT │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ │ └── params.character_Country.method_JOINT.model_EFT.tab │ │ │ │ ├── F81 │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ │ └── params.character_Country.method_JOINT.model_F81.tab │ │ │ │ └── JC │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ │ └── params.character_Country.method_JOINT.model_JC.tab │ │ │ ├── MAP │ │ │ │ ├── EFT │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── marginal_probabilities.character_Country.model_EFT.tab │ │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ │ └── params.character_Country.method_MAP.model_EFT.tab │ │ │ │ ├── F81 │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── marginal_probabilities.character_Country.model_F81.tab │ │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ │ └── params.character_Country.method_MAP.model_F81.tab │ │ │ │ └── JC │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── marginal_probabilities.character_Country.model_JC.tab │ │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ │ └── params.character_Country.method_MAP.model_JC.tab │ │ │ ├── ML │ │ │ │ ├── EFT │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── marginal_probabilities.character_Country_MAP.model_EFT.tab │ │ │ │ │ ├── marginal_probabilities.character_Country_MPPA.model_EFT.tab │ │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ │ ├── params.character_Country_JOINT.method_JOINT.model_EFT.tab │ │ │ │ │ ├── params.character_Country_MAP.method_MAP.model_EFT.tab │ │ │ │ │ └── params.character_Country_MPPA.method_MPPA.model_EFT.tab │ │ │ │ ├── F81 │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── marginal_probabilities.character_Country_MAP.model_F81.tab │ │ │ │ │ ├── marginal_probabilities.character_Country_MPPA.model_F81.tab │ │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ │ ├── params.character_Country_JOINT.method_JOINT.model_F81.tab │ │ │ │ │ ├── params.character_Country_MAP.method_MAP.model_F81.tab │ │ │ │ │ └── params.character_Country_MPPA.method_MPPA.model_F81.tab │ │ │ │ └── JC │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── marginal_probabilities.character_Country_MAP.model_JC.tab │ │ │ │ │ ├── marginal_probabilities.character_Country_MPPA.model_JC.tab │ │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ │ ├── params.character_Country_JOINT.method_JOINT.model_JC.tab │ │ │ │ │ ├── params.character_Country_MAP.method_MAP.model_JC.tab │ │ │ │ │ └── params.character_Country_MPPA.method_MPPA.model_JC.tab │ │ │ ├── MP │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ ├── params.character_Country_ACCTRAN.method_ACCTRAN.tab │ │ │ │ ├── params.character_Country_DELTRAN.method_DELTRAN.tab │ │ │ │ └── params.character_Country_DOWNPASS.method_DOWNPASS.tab │ │ │ ├── MPPA │ │ │ │ ├── EFT │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── marginal_probabilities.character_Country.model_EFT.tab │ │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ │ └── params.character_Country.method_MPPA.model_EFT.tab │ │ │ │ ├── F81 │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── marginal_probabilities.character_Country.model_F81.tab │ │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ │ └── params.character_Country.method_MPPA.model_F81.tab │ │ │ │ └── JC │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── marginal_probabilities.character_Country.model_JC.tab │ │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ │ └── params.character_Country.method_MPPA.model_JC.tab │ │ │ └── initial │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ ├── named.tree_Albanian.tree.152tax.tre │ │ │ │ └── params.character_Country.method_COPY.tab │ │ └── trees │ │ │ ├── Albanian_tree_ACCTRAN.html │ │ │ ├── Albanian_tree_ALL_EFT.html │ │ │ ├── Albanian_tree_ALL_F81.html │ │ │ ├── Albanian_tree_ALL_JC.html │ │ │ ├── Albanian_tree_COPY.html │ │ │ ├── Albanian_tree_DELTRAN.html │ │ │ ├── Albanian_tree_DOWNPASS.html │ │ │ ├── Albanian_tree_JOINT_EFT.html │ │ │ ├── Albanian_tree_JOINT_F81.html │ │ │ ├── Albanian_tree_JOINT_JC.html │ │ │ ├── Albanian_tree_MAP_EFT.html │ │ │ ├── Albanian_tree_MAP_F81.html │ │ │ ├── Albanian_tree_MAP_JC.html │ │ │ ├── Albanian_tree_ML_EFT.html │ │ │ ├── Albanian_tree_ML_F81.html │ │ │ ├── Albanian_tree_ML_JC.html │ │ │ ├── Albanian_tree_MP.html │ │ │ ├── Albanian_tree_MPPA_EFT.html │ │ │ ├── Albanian_tree_MPPA_F81.html │ │ │ ├── Albanian_tree_MPPA_JC.html │ │ │ └── Albanian_tree_initial.html │ └── main.py ├── DENV2 │ ├── README.md │ ├── data │ │ ├── maps │ │ │ ├── real │ │ │ │ ├── acr_map_Location.genotype_fast_tree.dated.html │ │ │ │ ├── acr_map_Location.genotype_phyml_tree.collapsed_support_0.5.dated.html │ │ │ │ ├── acr_map_Location.genotype_phyml_tree.dated.html │ │ │ │ ├── acr_map_Location.genotype_raxml_tree.dated.html │ │ │ │ ├── acr_map_Location_fast_tree.dated.html │ │ │ │ ├── acr_map_Location_phyml_tree.collapsed_support_0.5.dated.html │ │ │ │ ├── acr_map_Location_phyml_tree.dated.html │ │ │ │ ├── acr_map_Location_raxml_tree.dated.html │ │ │ │ ├── acr_tree_Location.genotype_fast_tree.dated.html │ │ │ │ ├── acr_tree_Location.genotype_phyml_tree.collapsed_support_0.5.dated.html │ │ │ │ ├── acr_tree_Location.genotype_phyml_tree.dated.html │ │ │ │ ├── acr_tree_Location.genotype_raxml_tree.dated.html │ │ │ │ ├── acr_tree_Location_fast_tree.dated.html │ │ │ │ ├── acr_tree_Location_phyml_tree.collapsed_support_0.5.dated.html │ │ │ │ ├── acr_tree_Location_phyml_tree.dated.html │ │ │ │ ├── acr_tree_Location_raxml_tree.dated.html │ │ │ │ └── geo_map_Location.html │ │ │ └── resampled │ │ │ │ ├── 0 │ │ │ │ ├── acr_map_Location_raxml_tree.dated.html │ │ │ │ ├── acr_tree_Location_raxml_tree.dated.html │ │ │ │ └── geo_map_Location.html │ │ │ │ ├── 1 │ │ │ │ ├── acr_map_Location_raxml_tree.dated.html │ │ │ │ ├── acr_tree_Location_raxml_tree.dated.html │ │ │ │ └── geo_map_Location.html │ │ │ │ ├── 2 │ │ │ │ ├── acr_map_Location_raxml_tree.dated.html │ │ │ │ ├── acr_tree_Location_raxml_tree.dated.html │ │ │ │ └── geo_map_Location.html │ │ │ │ ├── 3 │ │ │ │ ├── acr_map_Location_raxml_tree.dated.html │ │ │ │ ├── acr_tree_Location_raxml_tree.dated.html │ │ │ │ └── geo_map_Location.html │ │ │ │ └── 4 │ │ │ │ ├── acr_map_Location_raxml_tree.dated.html │ │ │ │ ├── acr_tree_Location_raxml_tree.dated.html │ │ │ │ └── geo_map_Location.html │ │ ├── pastml │ │ │ ├── real │ │ │ │ ├── fast_tree.dated │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── iTOL_colorstrip-Location.txt │ │ │ │ │ ├── iTOL_colorstrip-genotype.txt │ │ │ │ │ ├── iTOL_popup_info.txt │ │ │ │ │ ├── iTOL_style-Location.txt │ │ │ │ │ ├── iTOL_style-genotype.txt │ │ │ │ │ ├── iTOL_tree_id.txt │ │ │ │ │ ├── iTOL_url.txt │ │ │ │ │ ├── marginal_probabilities.character_Location.model_F81.tab │ │ │ │ │ ├── marginal_probabilities.character_genotype.model_F81.tab │ │ │ │ │ ├── named.tree_fast_tree.dated.nwk │ │ │ │ │ ├── params.character_Location.method_MPPA.model_F81.tab │ │ │ │ │ └── params.character_genotype.method_MPPA.model_F81.tab │ │ │ │ ├── phyml_tree.dated │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── iTOL_colorstrip-Location.txt │ │ │ │ │ ├── iTOL_colorstrip-genotype.txt │ │ │ │ │ ├── iTOL_popup_info.txt │ │ │ │ │ ├── iTOL_style-Location.txt │ │ │ │ │ ├── iTOL_style-genotype.txt │ │ │ │ │ ├── iTOL_tree_id.txt │ │ │ │ │ ├── iTOL_url.txt │ │ │ │ │ ├── marginal_probabilities.character_Location.model_F81.tab │ │ │ │ │ ├── marginal_probabilities.character_genotype.model_F81.tab │ │ │ │ │ ├── named.tree_phyml_tree.dated.nwk │ │ │ │ │ ├── params.character_Location.method_MPPA.model_F81.tab │ │ │ │ │ └── params.character_genotype.method_MPPA.model_F81.tab │ │ │ │ └── raxml_tree.dated │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── iTOL_colorstrip-Location.txt │ │ │ │ │ ├── iTOL_colorstrip-genotype.txt │ │ │ │ │ ├── iTOL_popup_info.txt │ │ │ │ │ ├── iTOL_style-Location.txt │ │ │ │ │ ├── iTOL_style-genotype.txt │ │ │ │ │ ├── iTOL_tree_id.txt │ │ │ │ │ ├── iTOL_url.txt │ │ │ │ │ ├── marginal_probabilities.character_Location.model_F81.tab │ │ │ │ │ ├── marginal_probabilities.character_genotype.model_F81.tab │ │ │ │ │ ├── named.tree_raxml_tree.dated.nwk │ │ │ │ │ ├── params.character_Location.method_MPPA.model_F81.tab │ │ │ │ │ └── params.character_genotype.method_MPPA.model_F81.tab │ │ │ └── resampled │ │ │ │ ├── 0 │ │ │ │ └── raxml_tree.dated │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── marginal_probabilities.character_Location.model_F81.tab │ │ │ │ │ ├── named.tree_raxml_tree.dated.nwk │ │ │ │ │ └── params.character_Location.method_MPPA.model_F81.tab │ │ │ │ ├── 1 │ │ │ │ └── raxml_tree.dated │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── marginal_probabilities.character_Location.model_F81.tab │ │ │ │ │ ├── named.tree_raxml_tree.dated.nwk │ │ │ │ │ └── params.character_Location.method_MPPA.model_F81.tab │ │ │ │ ├── 2 │ │ │ │ └── raxml_tree.dated │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── marginal_probabilities.character_Location.model_F81.tab │ │ │ │ │ ├── named.tree_raxml_tree.dated.nwk │ │ │ │ │ └── params.character_Location.method_MPPA.model_F81.tab │ │ │ │ ├── 3 │ │ │ │ └── raxml_tree.dated │ │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ │ ├── marginal_probabilities.character_Location.model_F81.tab │ │ │ │ │ ├── named.tree_raxml_tree.dated.nwk │ │ │ │ │ └── params.character_Location.method_MPPA.model_F81.tab │ │ │ │ └── 4 │ │ │ │ └── raxml_tree.dated │ │ │ │ ├── combined_ancestral_states.tab │ │ │ │ ├── marginal_probabilities.character_Location.model_F81.tab │ │ │ │ ├── named.tree_raxml_tree.dated.nwk │ │ │ │ └── params.character_Location.method_MPPA.model_F81.tab │ │ ├── real │ │ │ ├── all_trees.names │ │ │ ├── all_trees.nwk │ │ │ ├── aln.fa │ │ │ ├── aln.phylip │ │ │ ├── dates.tab │ │ │ ├── distances_all_trees.tab │ │ │ ├── fast_tree.dated.nwk │ │ │ ├── fast_tree.log │ │ │ ├── fast_tree.lsd.log │ │ │ ├── fast_tree.nwk │ │ │ ├── metadata.tab │ │ │ ├── phyml_tree.collapsed_support_0.5.dated.nwk │ │ │ ├── phyml_tree.collapsed_support_0.5.lsd.log │ │ │ ├── phyml_tree.dated.nwk │ │ │ ├── phyml_tree.log │ │ │ ├── phyml_tree.lsd.log │ │ │ ├── phyml_tree.nwk │ │ │ ├── raxml_tree.dated.nwk │ │ │ ├── raxml_tree.log │ │ │ ├── raxml_tree.lsd.log │ │ │ ├── raxml_tree.nwk │ │ │ └── raxml_tree.sh_support.nwk │ │ └── resampled │ │ │ ├── 0 │ │ │ ├── aln.fa │ │ │ ├── dates.tab │ │ │ ├── metadata.tab │ │ │ ├── raxml_tree.dated.nwk │ │ │ ├── raxml_tree.log │ │ │ ├── raxml_tree.lsd.log │ │ │ └── raxml_tree.nwk │ │ │ ├── 1 │ │ │ ├── aln.fa │ │ │ ├── dates.tab │ │ │ ├── metadata.tab │ │ │ ├── raxml_tree.dated.nwk │ │ │ ├── raxml_tree.log │ │ │ ├── raxml_tree.lsd.log │ │ │ └── raxml_tree.nwk │ │ │ ├── 2 │ │ │ ├── aln.fa │ │ │ ├── dates.tab │ │ │ ├── metadata.tab │ │ │ ├── raxml_tree.dated.nwk │ │ │ ├── raxml_tree.log │ │ │ ├── raxml_tree.lsd.log │ │ │ └── raxml_tree.nwk │ │ │ ├── 3 │ │ │ ├── aln.fa │ │ │ ├── dates.tab │ │ │ ├── metadata.tab │ │ │ ├── raxml_tree.dated.nwk │ │ │ ├── raxml_tree.log │ │ │ ├── raxml_tree.lsd.log │ │ │ └── raxml_tree.nwk │ │ │ ├── 4 │ │ │ ├── aln.fa │ │ │ ├── dates.tab │ │ │ ├── metadata.tab │ │ │ ├── raxml_tree.dated.nwk │ │ │ ├── raxml_tree.log │ │ │ ├── raxml_tree.lsd.log │ │ │ └── raxml_tree.nwk │ │ │ ├── distances_raxml_trees.tab │ │ │ └── distances_raxml_trees_vs_real.tab │ ├── main.py │ ├── py │ │ ├── collapse.py │ │ ├── compare_trees.py │ │ ├── convert_aln.py │ │ ├── extract_dates.py │ │ ├── merger.py │ │ ├── prune_trees.py │ │ └── resample_aln.py │ └── snakemake │ │ ├── Snakefile_acr │ │ ├── Snakefile_trees │ │ ├── pipeline_acr.svg │ │ └── pipeline_trees.svg ├── HIV1C │ ├── README.md │ ├── data │ │ ├── 0 │ │ │ ├── pars_tree.nwk │ │ │ ├── phyml_tree.log │ │ │ └── phyml_tree.nwk │ │ ├── 1 │ │ │ ├── pars_tree.nwk │ │ │ ├── phyml_tree.log │ │ │ └── phyml_tree.nwk │ │ ├── 2 │ │ │ ├── pars_tree.nwk │ │ │ ├── phyml_tree.log │ │ │ └── phyml_tree.nwk │ │ ├── 3 │ │ │ ├── pars_tree.nwk │ │ │ ├── phyml_tree.log │ │ │ └── phyml_tree.nwk │ │ ├── 4 │ │ │ ├── pars_tree.nwk │ │ │ ├── phyml_tree.log │ │ │ └── phyml_tree.nwk │ │ ├── HIV-1C.fasta │ │ ├── HIV-1C.tab │ │ ├── HIV1_ALL_2017_pol_DNA.fasta │ │ ├── aln.nodrm.fa │ │ ├── aln.nodrm.phylip │ │ ├── aln.nodrm.tnt │ │ ├── best │ │ │ ├── pastml_phyml_tree.nwk │ │ │ ├── phyml_tree.log │ │ │ └── phyml_tree.nwk │ │ ├── drm_data.tab.backup │ │ ├── ids_C.txt │ │ ├── maps │ │ │ └── Loc_Loc │ │ │ │ ├── geo_map_pastml_phyml_tree_Loc.html │ │ │ │ └── pastml_phyml_tree.html │ │ ├── metadata.tab │ │ ├── pars_trees.nex │ │ ├── pastml_params │ │ │ └── params.tree_pastml_phyml_tree.loc_Loc.tab │ │ └── prevalence.tab │ ├── main.py │ ├── py │ │ ├── acr.py │ │ ├── clean_aln.py │ │ ├── collapse.py │ │ ├── convert_aln.py │ │ ├── filter_aln_by_subtype.py │ │ ├── filter_unique_fasta_seq.py │ │ ├── find_TDR_root.py │ │ ├── get_best_tree.py │ │ ├── get_seq_ids.py │ │ ├── la_metadata.py │ │ ├── merge_md.py │ │ ├── name_tree.py │ │ ├── nex2nwk.py │ │ ├── prepare_metadata.py │ │ ├── prevalence.py │ │ ├── rename_phy.py │ │ ├── root.py │ │ └── timeline_tree.py │ └── snakemake │ │ ├── Snakefile_acr │ │ ├── Snakefile_trees │ │ ├── pipeline_acr.svg │ │ └── pipeline_trees.svg └── simulations │ ├── README.md │ ├── py │ ├── boxplot_params.py │ ├── name_tree.py │ ├── prepare_annotation.py │ └── read_params.py │ └── snakemake │ ├── Snakefile │ └── pipeline.svg ├── meta.yaml ├── pastml ├── __init__.py ├── acr.py ├── annotation.py ├── file.py ├── ml.py ├── models │ ├── CustomRatesModel.py │ ├── EFTModel.py │ ├── F81Model.py │ ├── HKYModel.py │ ├── JCModel.py │ ├── JTTModel.py │ ├── __init__.py │ └── generator.py ├── parsimony.py ├── templates │ ├── css │ │ ├── bootstrap.min.css │ │ ├── bootstrap.min.css.map │ │ └── jquery.qtip.min.css │ ├── fonts │ │ ├── glyphicons-halflings-regular.eot │ │ ├── glyphicons-halflings-regular.svg │ │ ├── glyphicons-halflings-regular.ttf │ │ ├── glyphicons-halflings-regular.woff │ │ └── glyphicons-halflings-regular.woff2 │ ├── geo_map.html │ ├── index.html │ ├── js │ │ ├── 0.0-jquery.min.js │ │ ├── 0.1-jquery.qtip.min.js │ │ ├── 1.1-cytoscape.min.js │ │ ├── 1.2-cytoscape-qtip.js │ │ ├── 1.3-cytoscape-svg.js │ │ ├── 1.4-layout-base.min.js │ │ ├── 1.5-cose-base.min.js │ │ ├── 1.6-cytoscape-cose-bilkent.min.js │ │ ├── bootstrap.min.js │ │ └── bootstrap.min.js.map │ ├── pie_tree.js │ ├── pie_tree_simple.js │ ├── time_slider.html │ └── transitions.js ├── tree.py ├── utilities │ ├── __init__.py │ ├── calculate_changes.py │ ├── state_simulator.py │ └── transition_counter.py └── visualisation │ ├── __init__.py │ ├── colour_generator.py │ ├── cytoscape_manager.py │ ├── generate_geomap.py │ ├── itol_manager.py │ └── tree_compressor.py ├── setup.py └── tests ├── ACRParameterOptimisationMPPAEFTTest.py ├── ACRParameterOptimisationMPPAF81Test.py ├── ACRParameterOptimisationMPPAJCTest.py ├── ACRStateAcctranTest.py ├── ACRStateCopyTest.py ├── ACRStateDeltranTest.py ├── ACRStateDownpassTest.py ├── ACRStateJointEFTTest.py ├── ACRStateJointF81Test.py ├── ACRStateJointJCTest.py ├── ACRStateMAPEFTTest.py ├── ACRStateMAPF81Test.py ├── ACRStateMAPJCTest.py ├── ACRStateMPPAEFTTest.py ├── ACRStateMPPAF81Test.py ├── ACRStateMPPAJCTest.py ├── CUSTOM_RATESTest.py ├── DateConversionTest.py ├── HKYF81Test.py ├── HKYJCTest.py ├── JTTTest.py ├── MRANDJCTest.py ├── PijTest.py └── data ├── Albanian.minitree.tre ├── Albanian.tree.152tax.tre ├── copy_states.tab ├── data.txt ├── dated_polytomy ├── locs.tab └── lsd2.nexus ├── params.character_Country.method_MPPA.model_JC.tab ├── tree.152taxa.sf_0.5.A_0.25.C_0.25.G_0.25.T_0.25.nwk ├── tree.152taxa.sf_0.5.A_0.25.C_0.25.G_0.25.T_0.25.pastml.tab ├── tree.152taxa.sf_0.5.A_0.6.C_0.15.G_0.2.T_0.05.nwk └── tree.152taxa.sf_0.5.A_0.6.C_0.15.G_0.2.T_0.05.pastml.tab /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- 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