Pandemic Sciences Institute: Pathogen Dynamics Group

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1. OpenABM-Covid19 OpenABM-Covid19 Public

   OpenABM-Covid19: an agent-based model for modelling the spread of SARS-CoV-2 (coronavirus) and control interventions for the Covid-19 epidemic

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2. covid-19_instant_tracing covid-19_instant_tracing Public

   Preprints from the BDI Pathogen Dynamics team regarding digital contact tracing and other non-pharmaceutical interventions for Covid-19. More details on our website:

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3. phyloscanner phyloscanner Public

   Phylogenetics between and within hosts at once, all along the genome.

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4. EpiLine EpiLine Public

   Bayesian Modelling in Epidemiology Case Line Lists

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5. covid-19_shiny covid-19_shiny Public

   Code for "Digital contact tracing for SARS-COV-2" shiny app

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6. POPART-IBM POPART-IBM Public

   C code of the individual-based model developed as part of the HPTN071 (PopART) trial

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