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diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
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diff --git a/examples/Albania/README.md b/examples/Albania/README.md
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diff --git a/examples/Albania/data/pastml/ACCTRAN/combined_ancestral_states.tab b/examples/Albania/data/pastml/ACCTRAN/combined_ancestral_states.tab
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diff --git a/examples/Albania/data/pastml/ACCTRAN/params.character_Country.method_ACCTRAN.tab b/examples/Albania/data/pastml/ACCTRAN/params.character_Country.method_ACCTRAN.tab
diff --git a/examples/Albania/data/pastml/ALL/EFT/combined_ancestral_states.tab b/examples/Albania/data/pastml/ALL/EFT/combined_ancestral_states.tab
diff --git a/examples/Albania/data/pastml/ALL/EFT/iTOL_colorstrip-Country_ACCTRAN.txt b/examples/Albania/data/pastml/ALL/EFT/iTOL_colorstrip-Country_ACCTRAN.txt
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diff --git a/examples/Albania/data/pastml/ALL/EFT/iTOL_colorstrip-Country_MAP.txt b/examples/Albania/data/pastml/ALL/EFT/iTOL_colorstrip-Country_MAP.txt
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diff --git a/...es/Albania/data/pastml/ALL/EFT/marginal_probabilities.character_Country_MAP.model_EFT.tab b/...es/Albania/data/pastml/ALL/EFT/marginal_probabilities.character_Country_MAP.model_EFT.tab
diff --git a/...s/Albania/data/pastml/ALL/EFT/marginal_probabilities.character_Country_MPPA.model_EFT.tab b/...s/Albania/data/pastml/ALL/EFT/marginal_probabilities.character_Country_MPPA.model_EFT.tab
diff --git a/examples/Albania/data/pastml/ALL/EFT/named.tree_Albanian.tree.152tax.tre b/examples/Albania/data/pastml/ALL/EFT/named.tree_Albanian.tree.152tax.tre
diff --git a/examples/Albania/data/pastml/ALL/EFT/params.character_Country_ACCTRAN.method_ACCTRAN.tab b/examples/Albania/data/pastml/ALL/EFT/params.character_Country_ACCTRAN.method_ACCTRAN.tab
diff --git a/examples/Albania/data/pastml/ALL/EFT/params.character_Country_DELTRAN.method_DELTRAN.tab b/examples/Albania/data/pastml/ALL/EFT/params.character_Country_DELTRAN.method_DELTRAN.tab
diff --git a/examples/Albania/data/pastml/ALL/EFT/params.character_Country_DOWNPASS.method_DOWNPASS.tab b/examples/Albania/data/pastml/ALL/EFT/params.character_Country_DOWNPASS.method_DOWNPASS.tab
diff --git a/...les/Albania/data/pastml/ALL/EFT/params.character_Country_JOINT.method_JOINT.model_EFT.tab b/...les/Albania/data/pastml/ALL/EFT/params.character_Country_JOINT.method_JOINT.model_EFT.tab
diff --git a/examples/Albania/data/pastml/ALL/EFT/params.character_Country_MAP.method_MAP.model_EFT.tab b/examples/Albania/data/pastml/ALL/EFT/params.character_Country_MAP.method_MAP.model_EFT.tab
diff --git a/examples/Albania/data/pastml/ALL/EFT/params.character_Country_MPPA.method_MPPA.model_EFT.tab b/examples/Albania/data/pastml/ALL/EFT/params.character_Country_MPPA.method_MPPA.model_EFT.tab
diff --git a/examples/Albania/data/pastml/ALL/F81/combined_ancestral_states.tab b/examples/Albania/data/pastml/ALL/F81/combined_ancestral_states.tab
diff --git a/examples/Albania/data/pastml/ALL/F81/iTOL_colorstrip-Country_ACCTRAN.txt b/examples/Albania/data/pastml/ALL/F81/iTOL_colorstrip-Country_ACCTRAN.txt
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diff --git a/examples/Albania/data/pastml/ALL/F81/iTOL_colorstrip-Country_DOWNPASS.txt b/examples/Albania/data/pastml/ALL/F81/iTOL_colorstrip-Country_DOWNPASS.txt
diff --git a/examples/Albania/data/pastml/ALL/F81/iTOL_colorstrip-Country_JOINT.txt b/examples/Albania/data/pastml/ALL/F81/iTOL_colorstrip-Country_JOINT.txt
diff --git a/examples/Albania/data/pastml/ALL/F81/iTOL_colorstrip-Country_MAP.txt b/examples/Albania/data/pastml/ALL/F81/iTOL_colorstrip-Country_MAP.txt
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diff --git a/examples/Albania/data/pastml/ALL/F81/iTOL_popup_info.txt b/examples/Albania/data/pastml/ALL/F81/iTOL_popup_info.txt
diff --git a/examples/Albania/data/pastml/ALL/F81/iTOL_style-Country_ACCTRAN.txt b/examples/Albania/data/pastml/ALL/F81/iTOL_style-Country_ACCTRAN.txt
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diff --git a/examples/Albania/data/pastml/ALL/F81/iTOL_style-Country_JOINT.txt b/examples/Albania/data/pastml/ALL/F81/iTOL_style-Country_JOINT.txt
diff --git a/examples/Albania/data/pastml/ALL/F81/iTOL_style-Country_MAP.txt b/examples/Albania/data/pastml/ALL/F81/iTOL_style-Country_MAP.txt
diff --git a/examples/Albania/data/pastml/ALL/F81/iTOL_style-Country_MPPA.txt b/examples/Albania/data/pastml/ALL/F81/iTOL_style-Country_MPPA.txt
diff --git a/examples/Albania/data/pastml/ALL/F81/iTOL_tree_id.txt b/examples/Albania/data/pastml/ALL/F81/iTOL_tree_id.txt
diff --git a/examples/Albania/data/pastml/ALL/F81/iTOL_url.txt b/examples/Albania/data/pastml/ALL/F81/iTOL_url.txt
diff --git a/...es/Albania/data/pastml/ALL/F81/marginal_probabilities.character_Country_MAP.model_F81.tab b/...es/Albania/data/pastml/ALL/F81/marginal_probabilities.character_Country_MAP.model_F81.tab
diff --git a/...s/Albania/data/pastml/ALL/F81/marginal_probabilities.character_Country_MPPA.model_F81.tab b/...s/Albania/data/pastml/ALL/F81/marginal_probabilities.character_Country_MPPA.model_F81.tab
diff --git a/examples/Albania/data/pastml/ALL/F81/named.tree_Albanian.tree.152tax.tre b/examples/Albania/data/pastml/ALL/F81/named.tree_Albanian.tree.152tax.tre
diff --git a/examples/Albania/data/pastml/ALL/F81/params.character_Country_ACCTRAN.method_ACCTRAN.tab b/examples/Albania/data/pastml/ALL/F81/params.character_Country_ACCTRAN.method_ACCTRAN.tab
diff --git a/examples/Albania/data/pastml/ALL/F81/params.character_Country_DELTRAN.method_DELTRAN.tab b/examples/Albania/data/pastml/ALL/F81/params.character_Country_DELTRAN.method_DELTRAN.tab
diff --git a/examples/Albania/data/pastml/ALL/F81/params.character_Country_DOWNPASS.method_DOWNPASS.tab b/examples/Albania/data/pastml/ALL/F81/params.character_Country_DOWNPASS.method_DOWNPASS.tab
diff --git a/...les/Albania/data/pastml/ALL/F81/params.character_Country_JOINT.method_JOINT.model_F81.tab b/...les/Albania/data/pastml/ALL/F81/params.character_Country_JOINT.method_JOINT.model_F81.tab
diff --git a/examples/Albania/data/pastml/ALL/F81/params.character_Country_MAP.method_MAP.model_F81.tab b/examples/Albania/data/pastml/ALL/F81/params.character_Country_MAP.method_MAP.model_F81.tab
diff --git a/examples/Albania/data/pastml/ALL/F81/params.character_Country_MPPA.method_MPPA.model_F81.tab b/examples/Albania/data/pastml/ALL/F81/params.character_Country_MPPA.method_MPPA.model_F81.tab
diff --git a/examples/Albania/data/pastml/ALL/JC/combined_ancestral_states.tab b/examples/Albania/data/pastml/ALL/JC/combined_ancestral_states.tab
diff --git a/examples/Albania/data/pastml/ALL/JC/iTOL_colorstrip-Country_ACCTRAN.txt b/examples/Albania/data/pastml/ALL/JC/iTOL_colorstrip-Country_ACCTRAN.txt
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diff --git a/examples/Albania/data/pastml/ALL/JC/iTOL_popup_info.txt b/examples/Albania/data/pastml/ALL/JC/iTOL_popup_info.txt
diff --git a/examples/Albania/data/pastml/ALL/JC/iTOL_style-Country_ACCTRAN.txt b/examples/Albania/data/pastml/ALL/JC/iTOL_style-Country_ACCTRAN.txt
diff --git a/examples/Albania/data/pastml/ALL/JC/iTOL_style-Country_DELTRAN.txt b/examples/Albania/data/pastml/ALL/JC/iTOL_style-Country_DELTRAN.txt
diff --git a/examples/Albania/data/pastml/ALL/JC/iTOL_style-Country_DOWNPASS.txt b/examples/Albania/data/pastml/ALL/JC/iTOL_style-Country_DOWNPASS.txt
diff --git a/examples/Albania/data/pastml/ALL/JC/iTOL_style-Country_JOINT.txt b/examples/Albania/data/pastml/ALL/JC/iTOL_style-Country_JOINT.txt
diff --git a/examples/Albania/data/pastml/ALL/JC/iTOL_style-Country_MAP.txt b/examples/Albania/data/pastml/ALL/JC/iTOL_style-Country_MAP.txt
diff --git a/examples/Albania/data/pastml/ALL/JC/iTOL_style-Country_MPPA.txt b/examples/Albania/data/pastml/ALL/JC/iTOL_style-Country_MPPA.txt
diff --git a/examples/Albania/data/pastml/ALL/JC/iTOL_tree_id.txt b/examples/Albania/data/pastml/ALL/JC/iTOL_tree_id.txt
diff --git a/examples/Albania/data/pastml/ALL/JC/iTOL_url.txt b/examples/Albania/data/pastml/ALL/JC/iTOL_url.txt
diff --git a/...ples/Albania/data/pastml/ALL/JC/marginal_probabilities.character_Country_MAP.model_JC.tab b/...ples/Albania/data/pastml/ALL/JC/marginal_probabilities.character_Country_MAP.model_JC.tab
diff --git a/...les/Albania/data/pastml/ALL/JC/marginal_probabilities.character_Country_MPPA.model_JC.tab b/...les/Albania/data/pastml/ALL/JC/marginal_probabilities.character_Country_MPPA.model_JC.tab
diff --git a/examples/Albania/data/pastml/ALL/JC/named.tree_Albanian.tree.152tax.tre b/examples/Albania/data/pastml/ALL/JC/named.tree_Albanian.tree.152tax.tre
diff --git a/examples/Albania/data/pastml/ALL/JC/params.character_Country_ACCTRAN.method_ACCTRAN.tab b/examples/Albania/data/pastml/ALL/JC/params.character_Country_ACCTRAN.method_ACCTRAN.tab
diff --git a/examples/Albania/data/pastml/ALL/JC/params.character_Country_DELTRAN.method_DELTRAN.tab b/examples/Albania/data/pastml/ALL/JC/params.character_Country_DELTRAN.method_DELTRAN.tab
diff --git a/examples/Albania/data/pastml/ALL/JC/params.character_Country_DOWNPASS.method_DOWNPASS.tab b/examples/Albania/data/pastml/ALL/JC/params.character_Country_DOWNPASS.method_DOWNPASS.tab
diff --git a/examples/Albania/data/pastml/ALL/JC/params.character_Country_JOINT.method_JOINT.model_JC.tab b/examples/Albania/data/pastml/ALL/JC/params.character_Country_JOINT.method_JOINT.model_JC.tab
diff --git a/examples/Albania/data/pastml/ALL/JC/params.character_Country_MAP.method_MAP.model_JC.tab b/examples/Albania/data/pastml/ALL/JC/params.character_Country_MAP.method_MAP.model_JC.tab
diff --git a/examples/Albania/data/pastml/ALL/JC/params.character_Country_MPPA.method_MPPA.model_JC.tab b/examples/Albania/data/pastml/ALL/JC/params.character_Country_MPPA.method_MPPA.model_JC.tab
diff --git a/examples/Albania/data/pastml/COPY/combined_ancestral_states.tab b/examples/Albania/data/pastml/COPY/combined_ancestral_states.tab
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diff --git a/examples/Albania/data/pastml/COPY/params.character_Country.method_COPY.tab b/examples/Albania/data/pastml/COPY/params.character_Country.method_COPY.tab
diff --git a/examples/Albania/data/pastml/DELTRAN/combined_ancestral_states.tab b/examples/Albania/data/pastml/DELTRAN/combined_ancestral_states.tab
diff --git a/examples/Albania/data/pastml/DELTRAN/named.tree_Albanian.tree.152tax.tre b/examples/Albania/data/pastml/DELTRAN/named.tree_Albanian.tree.152tax.tre
diff --git a/examples/Albania/data/pastml/DELTRAN/params.character_Country.method_DELTRAN.tab b/examples/Albania/data/pastml/DELTRAN/params.character_Country.method_DELTRAN.tab
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diff --git a/examples/Albania/data/pastml/DOWNPASS/params.character_Country.method_DOWNPASS.tab b/examples/Albania/data/pastml/DOWNPASS/params.character_Country.method_DOWNPASS.tab
diff --git a/examples/Albania/data/pastml/JOINT/EFT/combined_ancestral_states.tab b/examples/Albania/data/pastml/JOINT/EFT/combined_ancestral_states.tab
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diff --git a/examples/Albania/data/pastml/JOINT/EFT/params.character_Country.method_JOINT.model_EFT.tab b/examples/Albania/data/pastml/JOINT/EFT/params.character_Country.method_JOINT.model_EFT.tab
diff --git a/examples/Albania/data/pastml/JOINT/F81/combined_ancestral_states.tab b/examples/Albania/data/pastml/JOINT/F81/combined_ancestral_states.tab
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diff --git a/examples/Albania/data/pastml/JOINT/F81/params.character_Country.method_JOINT.model_F81.tab b/examples/Albania/data/pastml/JOINT/F81/params.character_Country.method_JOINT.model_F81.tab
diff --git a/examples/Albania/data/pastml/JOINT/JC/combined_ancestral_states.tab b/examples/Albania/data/pastml/JOINT/JC/combined_ancestral_states.tab
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diff --git a/examples/Albania/data/pastml/JOINT/JC/params.character_Country.method_JOINT.model_JC.tab b/examples/Albania/data/pastml/JOINT/JC/params.character_Country.method_JOINT.model_JC.tab
diff --git a/examples/Albania/data/pastml/MAP/EFT/combined_ancestral_states.tab b/examples/Albania/data/pastml/MAP/EFT/combined_ancestral_states.tab
diff --git a/examples/Albania/data/pastml/MAP/EFT/marginal_probabilities.character_Country.model_EFT.tab b/examples/Albania/data/pastml/MAP/EFT/marginal_probabilities.character_Country.model_EFT.tab
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diff --git a/examples/DENV2/data/pastml/real/phyml_tree.dated/iTOL_style-Location.txt b/examples/DENV2/data/pastml/real/phyml_tree.dated/iTOL_style-Location.txt
diff --git a/examples/DENV2/data/pastml/real/phyml_tree.dated/iTOL_style-genotype.txt b/examples/DENV2/data/pastml/real/phyml_tree.dated/iTOL_style-genotype.txt
diff --git a/examples/DENV2/data/pastml/real/phyml_tree.dated/iTOL_tree_id.txt b/examples/DENV2/data/pastml/real/phyml_tree.dated/iTOL_tree_id.txt
diff --git a/examples/DENV2/data/pastml/real/phyml_tree.dated/iTOL_url.txt b/examples/DENV2/data/pastml/real/phyml_tree.dated/iTOL_url.txt
diff --git a/...data/pastml/real/phyml_tree.dated/marginal_probabilities.character_Location.model_F81.tab b/...data/pastml/real/phyml_tree.dated/marginal_probabilities.character_Location.model_F81.tab
diff --git a/...data/pastml/real/phyml_tree.dated/marginal_probabilities.character_genotype.model_F81.tab b/...data/pastml/real/phyml_tree.dated/marginal_probabilities.character_genotype.model_F81.tab
diff --git a/examples/DENV2/data/pastml/real/phyml_tree.dated/named.tree_phyml_tree.dated.nwk b/examples/DENV2/data/pastml/real/phyml_tree.dated/named.tree_phyml_tree.dated.nwk
diff --git a/...NV2/data/pastml/real/phyml_tree.dated/params.character_Location.method_MPPA.model_F81.tab b/...NV2/data/pastml/real/phyml_tree.dated/params.character_Location.method_MPPA.model_F81.tab
diff --git a/...NV2/data/pastml/real/phyml_tree.dated/params.character_genotype.method_MPPA.model_F81.tab b/...NV2/data/pastml/real/phyml_tree.dated/params.character_genotype.method_MPPA.model_F81.tab
diff --git a/examples/DENV2/data/pastml/real/raxml_tree.dated/combined_ancestral_states.tab b/examples/DENV2/data/pastml/real/raxml_tree.dated/combined_ancestral_states.tab
diff --git a/examples/DENV2/data/pastml/real/raxml_tree.dated/iTOL_colorstrip-Location.txt b/examples/DENV2/data/pastml/real/raxml_tree.dated/iTOL_colorstrip-Location.txt
diff --git a/examples/DENV2/data/pastml/real/raxml_tree.dated/iTOL_colorstrip-genotype.txt b/examples/DENV2/data/pastml/real/raxml_tree.dated/iTOL_colorstrip-genotype.txt
diff --git a/examples/DENV2/data/pastml/real/raxml_tree.dated/iTOL_popup_info.txt b/examples/DENV2/data/pastml/real/raxml_tree.dated/iTOL_popup_info.txt
diff --git a/examples/DENV2/data/pastml/real/raxml_tree.dated/iTOL_style-Location.txt b/examples/DENV2/data/pastml/real/raxml_tree.dated/iTOL_style-Location.txt
diff --git a/examples/DENV2/data/pastml/real/raxml_tree.dated/iTOL_style-genotype.txt b/examples/DENV2/data/pastml/real/raxml_tree.dated/iTOL_style-genotype.txt
diff --git a/examples/DENV2/data/pastml/real/raxml_tree.dated/iTOL_tree_id.txt b/examples/DENV2/data/pastml/real/raxml_tree.dated/iTOL_tree_id.txt
diff --git a/examples/DENV2/data/pastml/real/raxml_tree.dated/iTOL_url.txt b/examples/DENV2/data/pastml/real/raxml_tree.dated/iTOL_url.txt
diff --git a/...data/pastml/real/raxml_tree.dated/marginal_probabilities.character_Location.model_F81.tab b/...data/pastml/real/raxml_tree.dated/marginal_probabilities.character_Location.model_F81.tab
diff --git a/...data/pastml/real/raxml_tree.dated/marginal_probabilities.character_genotype.model_F81.tab b/...data/pastml/real/raxml_tree.dated/marginal_probabilities.character_genotype.model_F81.tab
diff --git a/examples/DENV2/data/pastml/real/raxml_tree.dated/named.tree_raxml_tree.dated.nwk b/examples/DENV2/data/pastml/real/raxml_tree.dated/named.tree_raxml_tree.dated.nwk
diff --git a/...NV2/data/pastml/real/raxml_tree.dated/params.character_Location.method_MPPA.model_F81.tab b/...NV2/data/pastml/real/raxml_tree.dated/params.character_Location.method_MPPA.model_F81.tab
diff --git a/...NV2/data/pastml/real/raxml_tree.dated/params.character_genotype.method_MPPA.model_F81.tab b/...NV2/data/pastml/real/raxml_tree.dated/params.character_genotype.method_MPPA.model_F81.tab
diff --git a/examples/DENV2/data/pastml/resampled/0/raxml_tree.dated/combined_ancestral_states.tab b/examples/DENV2/data/pastml/resampled/0/raxml_tree.dated/combined_ancestral_states.tab
diff --git a/...stml/resampled/0/raxml_tree.dated/marginal_probabilities.character_Location.model_F81.tab b/...stml/resampled/0/raxml_tree.dated/marginal_probabilities.character_Location.model_F81.tab
diff --git a/examples/DENV2/data/pastml/resampled/0/raxml_tree.dated/named.tree_raxml_tree.dated.nwk b/examples/DENV2/data/pastml/resampled/0/raxml_tree.dated/named.tree_raxml_tree.dated.nwk
diff --git a/...a/pastml/resampled/0/raxml_tree.dated/params.character_Location.method_MPPA.model_F81.tab b/...a/pastml/resampled/0/raxml_tree.dated/params.character_Location.method_MPPA.model_F81.tab
diff --git a/examples/DENV2/data/pastml/resampled/1/raxml_tree.dated/combined_ancestral_states.tab b/examples/DENV2/data/pastml/resampled/1/raxml_tree.dated/combined_ancestral_states.tab
diff --git a/...stml/resampled/1/raxml_tree.dated/marginal_probabilities.character_Location.model_F81.tab b/...stml/resampled/1/raxml_tree.dated/marginal_probabilities.character_Location.model_F81.tab
diff --git a/examples/DENV2/data/pastml/resampled/1/raxml_tree.dated/named.tree_raxml_tree.dated.nwk b/examples/DENV2/data/pastml/resampled/1/raxml_tree.dated/named.tree_raxml_tree.dated.nwk
diff --git a/...a/pastml/resampled/1/raxml_tree.dated/params.character_Location.method_MPPA.model_F81.tab b/...a/pastml/resampled/1/raxml_tree.dated/params.character_Location.method_MPPA.model_F81.tab
diff --git a/examples/DENV2/data/pastml/resampled/2/raxml_tree.dated/combined_ancestral_states.tab b/examples/DENV2/data/pastml/resampled/2/raxml_tree.dated/combined_ancestral_states.tab
diff --git a/...stml/resampled/2/raxml_tree.dated/marginal_probabilities.character_Location.model_F81.tab b/...stml/resampled/2/raxml_tree.dated/marginal_probabilities.character_Location.model_F81.tab
diff --git a/examples/DENV2/data/pastml/resampled/2/raxml_tree.dated/named.tree_raxml_tree.dated.nwk b/examples/DENV2/data/pastml/resampled/2/raxml_tree.dated/named.tree_raxml_tree.dated.nwk
diff --git a/...a/pastml/resampled/2/raxml_tree.dated/params.character_Location.method_MPPA.model_F81.tab b/...a/pastml/resampled/2/raxml_tree.dated/params.character_Location.method_MPPA.model_F81.tab
diff --git a/examples/DENV2/data/pastml/resampled/3/raxml_tree.dated/combined_ancestral_states.tab b/examples/DENV2/data/pastml/resampled/3/raxml_tree.dated/combined_ancestral_states.tab
diff --git a/...stml/resampled/3/raxml_tree.dated/marginal_probabilities.character_Location.model_F81.tab b/...stml/resampled/3/raxml_tree.dated/marginal_probabilities.character_Location.model_F81.tab
diff --git a/examples/DENV2/data/pastml/resampled/3/raxml_tree.dated/named.tree_raxml_tree.dated.nwk b/examples/DENV2/data/pastml/resampled/3/raxml_tree.dated/named.tree_raxml_tree.dated.nwk
diff --git a/...a/pastml/resampled/3/raxml_tree.dated/params.character_Location.method_MPPA.model_F81.tab b/...a/pastml/resampled/3/raxml_tree.dated/params.character_Location.method_MPPA.model_F81.tab
diff --git a/examples/DENV2/data/pastml/resampled/4/raxml_tree.dated/combined_ancestral_states.tab b/examples/DENV2/data/pastml/resampled/4/raxml_tree.dated/combined_ancestral_states.tab
diff --git a/...stml/resampled/4/raxml_tree.dated/marginal_probabilities.character_Location.model_F81.tab b/...stml/resampled/4/raxml_tree.dated/marginal_probabilities.character_Location.model_F81.tab
diff --git a/examples/DENV2/data/pastml/resampled/4/raxml_tree.dated/named.tree_raxml_tree.dated.nwk b/examples/DENV2/data/pastml/resampled/4/raxml_tree.dated/named.tree_raxml_tree.dated.nwk
diff --git a/...a/pastml/resampled/4/raxml_tree.dated/params.character_Location.method_MPPA.model_F81.tab b/...a/pastml/resampled/4/raxml_tree.dated/params.character_Location.method_MPPA.model_F81.tab
diff --git a/examples/DENV2/data/real/all_trees.names b/examples/DENV2/data/real/all_trees.names
diff --git a/examples/DENV2/data/real/all_trees.nwk b/examples/DENV2/data/real/all_trees.nwk
diff --git a/examples/DENV2/data/real/aln.fa b/examples/DENV2/data/real/aln.fa
diff --git a/examples/DENV2/data/real/aln.phylip b/examples/DENV2/data/real/aln.phylip
diff --git a/examples/DENV2/data/real/dates.tab b/examples/DENV2/data/real/dates.tab
diff --git a/examples/DENV2/data/real/distances_all_trees.tab b/examples/DENV2/data/real/distances_all_trees.tab
diff --git a/examples/DENV2/data/real/fast_tree.dated.nwk b/examples/DENV2/data/real/fast_tree.dated.nwk
diff --git a/examples/DENV2/data/real/fast_tree.log b/examples/DENV2/data/real/fast_tree.log
diff --git a/examples/DENV2/data/real/fast_tree.lsd.log b/examples/DENV2/data/real/fast_tree.lsd.log
diff --git a/examples/DENV2/data/real/fast_tree.nwk b/examples/DENV2/data/real/fast_tree.nwk
diff --git a/examples/DENV2/data/real/metadata.tab b/examples/DENV2/data/real/metadata.tab