├── .gitignore ├── README.md ├── coalescent.html ├── flu.html ├── genomic-epi-sarscov2.html ├── images ├── 1918_beds.png ├── 1918_cases.png ├── ancestral_state_tree.png ├── beast_geo_ctmc.png ├── bernoulli_bayesian.png ├── bernoulli_ml.png ├── bmds_h3n2_diffusion_drift.png ├── bmds_h3n2_diffusion_map.png ├── bmds_h3n2_drift.jpg ├── bmds_h3n2_map.jpg ├── bmds_h3n2_tree.png ├── changing_pop_size_1.png ├── changing_pop_size_2.png ├── clock_flu_root_to_tip.png ├── clock_flu_timetree.png ├── clock_flu_tree.png ├── clock_zika_timings.png ├── coalescent_intervals_1.png ├── coalescent_intervals_2.png ├── coalescent_pop_size.png ├── coalescent_pop_size_2.png ├── coalescent_tree.png ├── coalescent_tree_shape.png ├── diversity.png ├── flight_network.jpg ├── flu_coalescence.png ├── flu_geo_h3_hist.png ├── flu_geo_h3_map.png ├── flu_geo_h3_sample_map.png ├── flu_geo_h3_trunk.png ├── flu_geo_predictors.png ├── flu_h3n2_tree.png ├── flu_h3n2_tree_vaccines.png ├── flu_seasonality.png ├── flu_trees.png ├── flu_vaccine_updates.png ├── flu_vs_measles_coalescence.png ├── hi_assay.png ├── hi_cross_reactivity.jpg ├── hi_full_table.png ├── hi_h3_map.png ├── hi_schematic.png ├── hi_smith_map.jpg ├── hi_table.png ├── hi_toy_distances.png ├── hi_toy_map.png ├── infection_tree_1.png ├── infection_tree_2.png ├── infection_tree_3.png ├── infection_tree_3b.png ├── infection_tree_4.png ├── infection_tree_4b.png ├── lifecycle.jpg ├── likelihood_tree_1.png ├── likelihood_tree_2.png ├── likelihood_tree_3.png ├── likelihood_tree_4.png ├── mcmc_1.png ├── mcmc_2.png ├── ncov_cryptic_transmission_outbreak_clade.png ├── ncov_cryptic_transmission_prevalence.png ├── ncov_data_quantity.png ├── ncov_early_tree_map_animation.mp4 ├── ncov_genomic_surveillance_dotplot_global_2021_09_12.png ├── ncov_sars_like_tree.png ├── ncov_tmrca_r0_2020_01_23.png ├── ncov_tree_2020_01_19.png ├── ncov_tree_2020_10_20_global_jun_oct.png ├── ncov_tree_map_2020_04_20_usa_1.png ├── ncov_tree_map_drc_2020_03_27.png ├── ncov_variants_animation_2021_09_12.gif ├── ncov_variants_emerging_lineages_2021_09_12.png ├── ncov_wa_phylodynamics_growth_rate.png ├── pandemics.png ├── pandemics_b.png ├── pandemics_na.png ├── parsimony_1.png ├── parsimony_2.png ├── parsimony_3.png ├── parsimony_4.png ├── parsimony_5.png ├── parsimony_exercise_1.png ├── parsimony_exercise_2.png ├── parsimony_exercise_3.png ├── parsimony_exercise_4.png ├── parsimony_exercise_5.png ├── parsimony_exercise_6.png ├── parsimony_exercise_7.png ├── parsimony_exercise_8.png ├── pathogen_phylogeny_ebola.png ├── pathogen_phylogeny_flu.png ├── pathogen_phylogeny_mers.jpg ├── phylogenetic_inference.png ├── phylogenetic_inference_alignment.png ├── phylogenetic_inference_site_patterns.png ├── phylogenetic_inference_solution_space.png ├── phylogenies_darwin.png ├── phylogenies_haeckel.jpg ├── phylogenies_pace.png ├── phylogenies_tudors.jpg ├── phylogeo_ebola_tree_map.png ├── phylogeo_flu_map.png ├── phylogeo_flu_tree.png ├── phylogeo_inference_data.png ├── phylogeo_inference_model.png ├── phylogeo_inference_nesting.png ├── phylogeo_inference_rare_transitions.png ├── phylogeo_zika_tree.png ├── reassortment.png ├── reassortment_swine.png ├── recombination_flu_b_railway.png ├── recombination_flu_b_trees.png ├── recombination_hiv_ld.png ├── recombination_hiv_trees.png ├── sarscov2_adaptive_evolution_dnds.png ├── sarscov2_adaptive_evolution_dnds_h3n2.png ├── sarscov2_adaptive_evolution_mut_accumulation_all_genes.png ├── sarscov2_adaptive_evolution_mut_accumulation_s1.png ├── sarscov2_adaptive_evolution_phylogeny.png ├── sarscov2_adaptive_evolution_phylogeny_logistic_growth.png ├── sarscov2_variant_rt_growth_advantage_2021_09_23.png ├── sarscov2_variant_rt_logistic_regression_2021_09_01.png ├── sarscov2_variant_rt_trajectories_2021_09_23.png ├── skyline.png ├── skyline_exercise_example_plot.png ├── skyline_exercise_example_tree.png ├── skyline_exercise_tree.png ├── skyline_flu.png ├── skyline_hcv.png ├── sneeze.gif ├── sneeze.jpg ├── spillover_ebola_tree.png ├── spillover_influenza_tree.png ├── spillover_mers_tree.png ├── tajima.png ├── tmrca.png ├── tree_episodic_selection.png ├── tree_negative_selection.png ├── tree_neutrality.png ├── tree_positive_selection.png ├── virion.jpg ├── wright_fisher_1.png ├── wright_fisher_2.png ├── wright_fisher_3.png ├── wright_fisher_4.png ├── wright_fisher_5.png ├── wright_fisher_6.png └── xkcd.png ├── intro.html ├── phylogenetics-and-virus-evolution.html ├── phylogenetics.html ├── reveal-v4 └── dist │ ├── reset.css │ ├── reveal.css │ ├── reveal.esm.js │ ├── reveal.js │ └── theme │ └── blotter.css └── reveal ├── css ├── font-awesome │ ├── css │ │ └── font-awesome.min.css │ └── fonts │ │ ├── FontAwesome.otf │ │ ├── fontawesome-webfont.eot │ │ ├── fontawesome-webfont.svg │ │ ├── fontawesome-webfont.ttf │ │ ├── fontawesome-webfont.woff │ │ └── fontawesome-webfont.woff2 ├── print │ ├── paper.css │ └── pdf.css ├── reveal.min.css └── theme │ ├── default.css │ ├── source │ ├── beige.scss │ ├── blood.scss │ ├── default.scss │ ├── moon.scss │ ├── night.scss │ ├── serif.scss │ ├── simple.scss │ ├── sky.scss │ └── solarized.scss │ ├── template │ ├── mixins.scss │ ├── settings.scss │ └── theme.scss │ └── trvrb.css ├── images └── logo.png ├── js ├── config.js └── reveal.min.js ├── lib ├── css │ └── zenburn.css ├── font │ ├── league_gothic-webfont.eot │ ├── league_gothic-webfont.svg │ ├── league_gothic-webfont.ttf │ ├── league_gothic-webfont.woff │ └── league_gothic_license └── js │ ├── classList.js │ ├── head.min.js │ └── html5shiv.js └── plugin ├── highlight └── highlight.js ├── leap └── leap.js ├── markdown ├── markdown.js └── marked.js ├── math └── math.js ├── multiplex ├── client.js ├── index.js └── master.js ├── notes-server ├── client.js ├── index.js └── notes.html ├── notes ├── notes.html └── notes.js ├── postmessage ├── example.html └── postmessage.js ├── print-pdf └── print-pdf.js ├── remotes └── remotes.js ├── search └── search.js └── zoom-js └── zoom.js /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/README.md -------------------------------------------------------------------------------- /coalescent.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/coalescent.html -------------------------------------------------------------------------------- /flu.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/flu.html -------------------------------------------------------------------------------- /genomic-epi-sarscov2.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/genomic-epi-sarscov2.html -------------------------------------------------------------------------------- /images/1918_beds.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/1918_beds.png -------------------------------------------------------------------------------- /images/1918_cases.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/1918_cases.png -------------------------------------------------------------------------------- /images/ancestral_state_tree.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/ancestral_state_tree.png -------------------------------------------------------------------------------- /images/beast_geo_ctmc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/beast_geo_ctmc.png -------------------------------------------------------------------------------- /images/bernoulli_bayesian.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/bernoulli_bayesian.png -------------------------------------------------------------------------------- /images/bernoulli_ml.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/bernoulli_ml.png -------------------------------------------------------------------------------- /images/bmds_h3n2_diffusion_drift.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/bmds_h3n2_diffusion_drift.png -------------------------------------------------------------------------------- /images/bmds_h3n2_diffusion_map.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/bmds_h3n2_diffusion_map.png -------------------------------------------------------------------------------- /images/bmds_h3n2_drift.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/bmds_h3n2_drift.jpg -------------------------------------------------------------------------------- /images/bmds_h3n2_map.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/bmds_h3n2_map.jpg -------------------------------------------------------------------------------- /images/bmds_h3n2_tree.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/bmds_h3n2_tree.png -------------------------------------------------------------------------------- /images/changing_pop_size_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/changing_pop_size_1.png -------------------------------------------------------------------------------- /images/changing_pop_size_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/changing_pop_size_2.png -------------------------------------------------------------------------------- /images/clock_flu_root_to_tip.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/clock_flu_root_to_tip.png -------------------------------------------------------------------------------- /images/clock_flu_timetree.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/clock_flu_timetree.png -------------------------------------------------------------------------------- /images/clock_flu_tree.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/clock_flu_tree.png -------------------------------------------------------------------------------- /images/clock_zika_timings.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/clock_zika_timings.png -------------------------------------------------------------------------------- /images/coalescent_intervals_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/coalescent_intervals_1.png -------------------------------------------------------------------------------- /images/coalescent_intervals_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/coalescent_intervals_2.png -------------------------------------------------------------------------------- /images/coalescent_pop_size.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/coalescent_pop_size.png -------------------------------------------------------------------------------- /images/coalescent_pop_size_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/coalescent_pop_size_2.png -------------------------------------------------------------------------------- /images/coalescent_tree.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/coalescent_tree.png -------------------------------------------------------------------------------- /images/coalescent_tree_shape.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/coalescent_tree_shape.png -------------------------------------------------------------------------------- /images/diversity.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/diversity.png -------------------------------------------------------------------------------- /images/flight_network.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/flight_network.jpg -------------------------------------------------------------------------------- /images/flu_coalescence.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/flu_coalescence.png -------------------------------------------------------------------------------- /images/flu_geo_h3_hist.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/flu_geo_h3_hist.png -------------------------------------------------------------------------------- /images/flu_geo_h3_map.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/flu_geo_h3_map.png -------------------------------------------------------------------------------- /images/flu_geo_h3_sample_map.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/flu_geo_h3_sample_map.png -------------------------------------------------------------------------------- /images/flu_geo_h3_trunk.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/flu_geo_h3_trunk.png -------------------------------------------------------------------------------- /images/flu_geo_predictors.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/flu_geo_predictors.png -------------------------------------------------------------------------------- /images/flu_h3n2_tree.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/flu_h3n2_tree.png -------------------------------------------------------------------------------- /images/flu_h3n2_tree_vaccines.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/flu_h3n2_tree_vaccines.png -------------------------------------------------------------------------------- /images/flu_seasonality.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/flu_seasonality.png -------------------------------------------------------------------------------- /images/flu_trees.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/flu_trees.png -------------------------------------------------------------------------------- /images/flu_vaccine_updates.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/flu_vaccine_updates.png -------------------------------------------------------------------------------- /images/flu_vs_measles_coalescence.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/flu_vs_measles_coalescence.png -------------------------------------------------------------------------------- /images/hi_assay.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/hi_assay.png -------------------------------------------------------------------------------- /images/hi_cross_reactivity.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/hi_cross_reactivity.jpg -------------------------------------------------------------------------------- /images/hi_full_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/hi_full_table.png -------------------------------------------------------------------------------- /images/hi_h3_map.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/hi_h3_map.png -------------------------------------------------------------------------------- /images/hi_schematic.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/hi_schematic.png -------------------------------------------------------------------------------- /images/hi_smith_map.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/hi_smith_map.jpg -------------------------------------------------------------------------------- /images/hi_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/hi_table.png -------------------------------------------------------------------------------- /images/hi_toy_distances.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/hi_toy_distances.png -------------------------------------------------------------------------------- /images/hi_toy_map.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/hi_toy_map.png -------------------------------------------------------------------------------- /images/infection_tree_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/infection_tree_1.png -------------------------------------------------------------------------------- /images/infection_tree_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/infection_tree_2.png -------------------------------------------------------------------------------- /images/infection_tree_3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/infection_tree_3.png -------------------------------------------------------------------------------- /images/infection_tree_3b.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/infection_tree_3b.png -------------------------------------------------------------------------------- /images/infection_tree_4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/infection_tree_4.png -------------------------------------------------------------------------------- /images/infection_tree_4b.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/infection_tree_4b.png -------------------------------------------------------------------------------- /images/lifecycle.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/lifecycle.jpg -------------------------------------------------------------------------------- /images/likelihood_tree_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/likelihood_tree_1.png -------------------------------------------------------------------------------- /images/likelihood_tree_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/likelihood_tree_2.png -------------------------------------------------------------------------------- /images/likelihood_tree_3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/likelihood_tree_3.png -------------------------------------------------------------------------------- /images/likelihood_tree_4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/likelihood_tree_4.png -------------------------------------------------------------------------------- /images/mcmc_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/mcmc_1.png -------------------------------------------------------------------------------- /images/mcmc_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/mcmc_2.png -------------------------------------------------------------------------------- /images/ncov_cryptic_transmission_outbreak_clade.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/ncov_cryptic_transmission_outbreak_clade.png -------------------------------------------------------------------------------- /images/ncov_cryptic_transmission_prevalence.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/ncov_cryptic_transmission_prevalence.png -------------------------------------------------------------------------------- /images/ncov_data_quantity.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/ncov_data_quantity.png -------------------------------------------------------------------------------- /images/ncov_early_tree_map_animation.mp4: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/ncov_early_tree_map_animation.mp4 -------------------------------------------------------------------------------- /images/ncov_genomic_surveillance_dotplot_global_2021_09_12.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/ncov_genomic_surveillance_dotplot_global_2021_09_12.png -------------------------------------------------------------------------------- /images/ncov_sars_like_tree.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/ncov_sars_like_tree.png -------------------------------------------------------------------------------- /images/ncov_tmrca_r0_2020_01_23.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/ncov_tmrca_r0_2020_01_23.png -------------------------------------------------------------------------------- /images/ncov_tree_2020_01_19.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/ncov_tree_2020_01_19.png -------------------------------------------------------------------------------- /images/ncov_tree_2020_10_20_global_jun_oct.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/ncov_tree_2020_10_20_global_jun_oct.png -------------------------------------------------------------------------------- /images/ncov_tree_map_2020_04_20_usa_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/ncov_tree_map_2020_04_20_usa_1.png -------------------------------------------------------------------------------- /images/ncov_tree_map_drc_2020_03_27.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/ncov_tree_map_drc_2020_03_27.png -------------------------------------------------------------------------------- /images/ncov_variants_animation_2021_09_12.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/ncov_variants_animation_2021_09_12.gif -------------------------------------------------------------------------------- /images/ncov_variants_emerging_lineages_2021_09_12.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/ncov_variants_emerging_lineages_2021_09_12.png -------------------------------------------------------------------------------- /images/ncov_wa_phylodynamics_growth_rate.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/ncov_wa_phylodynamics_growth_rate.png -------------------------------------------------------------------------------- /images/pandemics.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/pandemics.png -------------------------------------------------------------------------------- /images/pandemics_b.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/pandemics_b.png -------------------------------------------------------------------------------- /images/pandemics_na.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/pandemics_na.png -------------------------------------------------------------------------------- /images/parsimony_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/parsimony_1.png -------------------------------------------------------------------------------- /images/parsimony_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/parsimony_2.png -------------------------------------------------------------------------------- /images/parsimony_3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/parsimony_3.png -------------------------------------------------------------------------------- /images/parsimony_4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/parsimony_4.png -------------------------------------------------------------------------------- /images/parsimony_5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/parsimony_5.png -------------------------------------------------------------------------------- /images/parsimony_exercise_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/parsimony_exercise_1.png -------------------------------------------------------------------------------- /images/parsimony_exercise_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/parsimony_exercise_2.png -------------------------------------------------------------------------------- /images/parsimony_exercise_3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/parsimony_exercise_3.png -------------------------------------------------------------------------------- /images/parsimony_exercise_4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/parsimony_exercise_4.png -------------------------------------------------------------------------------- /images/parsimony_exercise_5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/parsimony_exercise_5.png -------------------------------------------------------------------------------- /images/parsimony_exercise_6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/parsimony_exercise_6.png -------------------------------------------------------------------------------- /images/parsimony_exercise_7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/parsimony_exercise_7.png -------------------------------------------------------------------------------- /images/parsimony_exercise_8.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/parsimony_exercise_8.png -------------------------------------------------------------------------------- /images/pathogen_phylogeny_ebola.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/pathogen_phylogeny_ebola.png -------------------------------------------------------------------------------- /images/pathogen_phylogeny_flu.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/pathogen_phylogeny_flu.png -------------------------------------------------------------------------------- /images/pathogen_phylogeny_mers.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/pathogen_phylogeny_mers.jpg -------------------------------------------------------------------------------- /images/phylogenetic_inference.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/phylogenetic_inference.png -------------------------------------------------------------------------------- /images/phylogenetic_inference_alignment.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/phylogenetic_inference_alignment.png -------------------------------------------------------------------------------- /images/phylogenetic_inference_site_patterns.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/phylogenetic_inference_site_patterns.png -------------------------------------------------------------------------------- /images/phylogenetic_inference_solution_space.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/phylogenetic_inference_solution_space.png -------------------------------------------------------------------------------- /images/phylogenies_darwin.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/phylogenies_darwin.png -------------------------------------------------------------------------------- /images/phylogenies_haeckel.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/phylogenies_haeckel.jpg -------------------------------------------------------------------------------- /images/phylogenies_pace.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/phylogenies_pace.png -------------------------------------------------------------------------------- /images/phylogenies_tudors.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/phylogenies_tudors.jpg -------------------------------------------------------------------------------- /images/phylogeo_ebola_tree_map.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/phylogeo_ebola_tree_map.png -------------------------------------------------------------------------------- /images/phylogeo_flu_map.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/phylogeo_flu_map.png -------------------------------------------------------------------------------- /images/phylogeo_flu_tree.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/phylogeo_flu_tree.png -------------------------------------------------------------------------------- /images/phylogeo_inference_data.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/phylogeo_inference_data.png -------------------------------------------------------------------------------- /images/phylogeo_inference_model.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/phylogeo_inference_model.png -------------------------------------------------------------------------------- /images/phylogeo_inference_nesting.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/phylogeo_inference_nesting.png -------------------------------------------------------------------------------- /images/phylogeo_inference_rare_transitions.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/phylogeo_inference_rare_transitions.png -------------------------------------------------------------------------------- /images/phylogeo_zika_tree.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/phylogeo_zika_tree.png -------------------------------------------------------------------------------- /images/reassortment.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/reassortment.png -------------------------------------------------------------------------------- /images/reassortment_swine.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/reassortment_swine.png -------------------------------------------------------------------------------- /images/recombination_flu_b_railway.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/recombination_flu_b_railway.png -------------------------------------------------------------------------------- /images/recombination_flu_b_trees.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/recombination_flu_b_trees.png -------------------------------------------------------------------------------- /images/recombination_hiv_ld.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/recombination_hiv_ld.png -------------------------------------------------------------------------------- /images/recombination_hiv_trees.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/recombination_hiv_trees.png -------------------------------------------------------------------------------- /images/sarscov2_adaptive_evolution_dnds.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/sarscov2_adaptive_evolution_dnds.png -------------------------------------------------------------------------------- /images/sarscov2_adaptive_evolution_dnds_h3n2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/sarscov2_adaptive_evolution_dnds_h3n2.png -------------------------------------------------------------------------------- /images/sarscov2_adaptive_evolution_mut_accumulation_all_genes.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/sarscov2_adaptive_evolution_mut_accumulation_all_genes.png -------------------------------------------------------------------------------- /images/sarscov2_adaptive_evolution_mut_accumulation_s1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/sarscov2_adaptive_evolution_mut_accumulation_s1.png -------------------------------------------------------------------------------- /images/sarscov2_adaptive_evolution_phylogeny.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/sarscov2_adaptive_evolution_phylogeny.png -------------------------------------------------------------------------------- /images/sarscov2_adaptive_evolution_phylogeny_logistic_growth.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/sarscov2_adaptive_evolution_phylogeny_logistic_growth.png -------------------------------------------------------------------------------- /images/sarscov2_variant_rt_growth_advantage_2021_09_23.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/sarscov2_variant_rt_growth_advantage_2021_09_23.png -------------------------------------------------------------------------------- /images/sarscov2_variant_rt_logistic_regression_2021_09_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/sarscov2_variant_rt_logistic_regression_2021_09_01.png -------------------------------------------------------------------------------- /images/sarscov2_variant_rt_trajectories_2021_09_23.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/sarscov2_variant_rt_trajectories_2021_09_23.png -------------------------------------------------------------------------------- /images/skyline.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/skyline.png -------------------------------------------------------------------------------- /images/skyline_exercise_example_plot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/skyline_exercise_example_plot.png -------------------------------------------------------------------------------- /images/skyline_exercise_example_tree.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/skyline_exercise_example_tree.png -------------------------------------------------------------------------------- /images/skyline_exercise_tree.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/skyline_exercise_tree.png -------------------------------------------------------------------------------- /images/skyline_flu.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/skyline_flu.png -------------------------------------------------------------------------------- /images/skyline_hcv.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/skyline_hcv.png -------------------------------------------------------------------------------- /images/sneeze.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/sneeze.gif -------------------------------------------------------------------------------- /images/sneeze.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/sneeze.jpg -------------------------------------------------------------------------------- /images/spillover_ebola_tree.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/spillover_ebola_tree.png -------------------------------------------------------------------------------- /images/spillover_influenza_tree.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/spillover_influenza_tree.png -------------------------------------------------------------------------------- /images/spillover_mers_tree.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/spillover_mers_tree.png -------------------------------------------------------------------------------- /images/tajima.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/tajima.png -------------------------------------------------------------------------------- /images/tmrca.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/tmrca.png -------------------------------------------------------------------------------- /images/tree_episodic_selection.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/tree_episodic_selection.png -------------------------------------------------------------------------------- /images/tree_negative_selection.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/tree_negative_selection.png -------------------------------------------------------------------------------- /images/tree_neutrality.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/tree_neutrality.png -------------------------------------------------------------------------------- /images/tree_positive_selection.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/tree_positive_selection.png -------------------------------------------------------------------------------- /images/virion.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/virion.jpg -------------------------------------------------------------------------------- /images/wright_fisher_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/wright_fisher_1.png -------------------------------------------------------------------------------- /images/wright_fisher_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/wright_fisher_2.png -------------------------------------------------------------------------------- /images/wright_fisher_3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/wright_fisher_3.png -------------------------------------------------------------------------------- /images/wright_fisher_4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/wright_fisher_4.png -------------------------------------------------------------------------------- /images/wright_fisher_5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/wright_fisher_5.png -------------------------------------------------------------------------------- /images/wright_fisher_6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/wright_fisher_6.png -------------------------------------------------------------------------------- /images/xkcd.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/images/xkcd.png -------------------------------------------------------------------------------- /intro.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/intro.html -------------------------------------------------------------------------------- /phylogenetics-and-virus-evolution.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/phylogenetics-and-virus-evolution.html -------------------------------------------------------------------------------- /phylogenetics.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/phylogenetics.html -------------------------------------------------------------------------------- /reveal-v4/dist/reset.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal-v4/dist/reset.css -------------------------------------------------------------------------------- /reveal-v4/dist/reveal.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal-v4/dist/reveal.css -------------------------------------------------------------------------------- /reveal-v4/dist/reveal.esm.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal-v4/dist/reveal.esm.js -------------------------------------------------------------------------------- /reveal-v4/dist/reveal.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal-v4/dist/reveal.js -------------------------------------------------------------------------------- /reveal-v4/dist/theme/blotter.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal-v4/dist/theme/blotter.css -------------------------------------------------------------------------------- /reveal/css/font-awesome/css/font-awesome.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/font-awesome/css/font-awesome.min.css -------------------------------------------------------------------------------- /reveal/css/font-awesome/fonts/FontAwesome.otf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/font-awesome/fonts/FontAwesome.otf -------------------------------------------------------------------------------- /reveal/css/font-awesome/fonts/fontawesome-webfont.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/font-awesome/fonts/fontawesome-webfont.eot -------------------------------------------------------------------------------- /reveal/css/font-awesome/fonts/fontawesome-webfont.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/font-awesome/fonts/fontawesome-webfont.svg -------------------------------------------------------------------------------- /reveal/css/font-awesome/fonts/fontawesome-webfont.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/font-awesome/fonts/fontawesome-webfont.ttf -------------------------------------------------------------------------------- /reveal/css/font-awesome/fonts/fontawesome-webfont.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/font-awesome/fonts/fontawesome-webfont.woff -------------------------------------------------------------------------------- /reveal/css/font-awesome/fonts/fontawesome-webfont.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/font-awesome/fonts/fontawesome-webfont.woff2 -------------------------------------------------------------------------------- /reveal/css/print/paper.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/print/paper.css -------------------------------------------------------------------------------- /reveal/css/print/pdf.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/print/pdf.css -------------------------------------------------------------------------------- /reveal/css/reveal.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/reveal.min.css -------------------------------------------------------------------------------- /reveal/css/theme/default.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/theme/default.css -------------------------------------------------------------------------------- /reveal/css/theme/source/beige.scss: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/theme/source/beige.scss -------------------------------------------------------------------------------- /reveal/css/theme/source/blood.scss: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/theme/source/blood.scss -------------------------------------------------------------------------------- /reveal/css/theme/source/default.scss: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/theme/source/default.scss -------------------------------------------------------------------------------- /reveal/css/theme/source/moon.scss: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/theme/source/moon.scss -------------------------------------------------------------------------------- /reveal/css/theme/source/night.scss: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/theme/source/night.scss -------------------------------------------------------------------------------- /reveal/css/theme/source/serif.scss: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/theme/source/serif.scss -------------------------------------------------------------------------------- /reveal/css/theme/source/simple.scss: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/theme/source/simple.scss -------------------------------------------------------------------------------- /reveal/css/theme/source/sky.scss: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/theme/source/sky.scss -------------------------------------------------------------------------------- /reveal/css/theme/source/solarized.scss: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/theme/source/solarized.scss -------------------------------------------------------------------------------- /reveal/css/theme/template/mixins.scss: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/theme/template/mixins.scss -------------------------------------------------------------------------------- /reveal/css/theme/template/settings.scss: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/theme/template/settings.scss -------------------------------------------------------------------------------- /reveal/css/theme/template/theme.scss: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/theme/template/theme.scss -------------------------------------------------------------------------------- /reveal/css/theme/trvrb.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/css/theme/trvrb.css -------------------------------------------------------------------------------- /reveal/images/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/images/logo.png -------------------------------------------------------------------------------- /reveal/js/config.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/js/config.js -------------------------------------------------------------------------------- /reveal/js/reveal.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/js/reveal.min.js -------------------------------------------------------------------------------- /reveal/lib/css/zenburn.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/lib/css/zenburn.css -------------------------------------------------------------------------------- /reveal/lib/font/league_gothic-webfont.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/lib/font/league_gothic-webfont.eot -------------------------------------------------------------------------------- /reveal/lib/font/league_gothic-webfont.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/lib/font/league_gothic-webfont.svg -------------------------------------------------------------------------------- /reveal/lib/font/league_gothic-webfont.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/lib/font/league_gothic-webfont.ttf -------------------------------------------------------------------------------- /reveal/lib/font/league_gothic-webfont.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/lib/font/league_gothic-webfont.woff -------------------------------------------------------------------------------- /reveal/lib/font/league_gothic_license: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/lib/font/league_gothic_license -------------------------------------------------------------------------------- /reveal/lib/js/classList.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/lib/js/classList.js -------------------------------------------------------------------------------- /reveal/lib/js/head.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/lib/js/head.min.js -------------------------------------------------------------------------------- /reveal/lib/js/html5shiv.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/lib/js/html5shiv.js -------------------------------------------------------------------------------- /reveal/plugin/highlight/highlight.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/highlight/highlight.js -------------------------------------------------------------------------------- /reveal/plugin/leap/leap.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/leap/leap.js -------------------------------------------------------------------------------- /reveal/plugin/markdown/markdown.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/markdown/markdown.js -------------------------------------------------------------------------------- /reveal/plugin/markdown/marked.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/markdown/marked.js -------------------------------------------------------------------------------- /reveal/plugin/math/math.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/math/math.js -------------------------------------------------------------------------------- /reveal/plugin/multiplex/client.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/multiplex/client.js -------------------------------------------------------------------------------- /reveal/plugin/multiplex/index.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/multiplex/index.js -------------------------------------------------------------------------------- /reveal/plugin/multiplex/master.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/multiplex/master.js -------------------------------------------------------------------------------- /reveal/plugin/notes-server/client.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/notes-server/client.js -------------------------------------------------------------------------------- /reveal/plugin/notes-server/index.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/notes-server/index.js -------------------------------------------------------------------------------- /reveal/plugin/notes-server/notes.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/notes-server/notes.html -------------------------------------------------------------------------------- /reveal/plugin/notes/notes.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/notes/notes.html -------------------------------------------------------------------------------- /reveal/plugin/notes/notes.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/notes/notes.js -------------------------------------------------------------------------------- /reveal/plugin/postmessage/example.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/postmessage/example.html -------------------------------------------------------------------------------- /reveal/plugin/postmessage/postmessage.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/postmessage/postmessage.js -------------------------------------------------------------------------------- /reveal/plugin/print-pdf/print-pdf.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/print-pdf/print-pdf.js -------------------------------------------------------------------------------- /reveal/plugin/remotes/remotes.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/remotes/remotes.js -------------------------------------------------------------------------------- /reveal/plugin/search/search.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/search/search.js -------------------------------------------------------------------------------- /reveal/plugin/zoom-js/zoom.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/phylodynamics-lecture/HEAD/reveal/plugin/zoom-js/zoom.js --------------------------------------------------------------------------------