Repositories list

• marburg-virus

  Public
  Nextstrain build of the Orthomarburgvirus marburgense species taxon

  Python

  •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• Quantification-of-the-spread-of-a-SARS-CoV-2-variant

  Public
  covid-19

  Python

  •

  GNU General Public License v3.0

  •0•10•0•0•Updated May 28, 2023May 28, 2023

• harvester-database-and-automation

  Public
  The database and automation infrastructure used in the Swiss SARS-CoV-2 Sequencing Consortium (S3C)

  automationresearchgenomics+ 2data-managementsars-cov-2

  Java

  •

  GNU Lesser General Public License v3.0

  •0•0•0•0•Updated May 16, 2023May 16, 2023

• Grapevine-SARS-CoV-2-Introduction-Analysis

  Public
  Pipeline for estimating putatively independent introductions of SARS-CoV-2 from genome sequences.

  R

  •0•0•0•0•Updated Oct 27, 2022Oct 27, 2022

• POUMM-GWAS

  Public
  Scripts for "A phylogeny-aware GWAS framework to correct for heritable pathogen effects on infectious disease traits".

  TeX

  •1•2•0•0•Updated Jul 21, 2022Jul 21, 2022

• 2018-StadlerEtAl-LineageTrees-CodeData

  Public
  0•0•0•0•Updated Jul 14, 2020Jul 14, 2020

• TreePrior-ClockRate

  Public
  Scripts and data for "The impact of the tree prior on estimating clock rates during epidemic outbreaks" (PNAS 2018)

  R

  •3•2•0•0•Updated Mar 18, 2018Mar 18, 2018

• 2015-GEMP-Phylodynamics

  Public
  Inferring epidemiological parameters from phylogenies with BEAST2

  1•0•0•0•Updated Sep 3, 2015Sep 3, 2015

• Ebola-CurrentsOutbreaks2014

  Public
  Additional files for our paper "Insights into the early epidemic spread of Ebola in Sierra Leone provided by viral sequence data" submitted to PLOS Currents Outbreaks in September 2014.

  R

  •

  MIT License

  •0•0•0•0•Updated Mar 26, 2015Mar 26, 2015

• 2015-CeskyKrumlov-Phylodynamics

  Public
  Český Krumlov 2015 - Phylodynamics

  R

  •2•2•0•0•Updated Feb 5, 2015Feb 5, 2015

• TreePar-MatlabPlugin

  Public
  Matlab plugin for TreePar to calculate likelihood for age dependent extinction rates

  M

  •

  GNU General Public License v2.0

  •0•1•0•0•Updated Nov 9, 2014Nov 9, 2014