neherlab

Repositories

• covid19_scenarios

  Models of COVID-19 outbreak trajectories and hospital demand

  open-source science data opensource research simulation model
  JavaScript MIT 372 1,370 37 (28 issues need help) 7 Updated Aug 1, 2021

• nextclade

  Forked from nextstrain/nextclade

  Assign SARS-CoV-2 clades in the browser
  TypeScript MIT 39 0 0 0 Updated Jul 30, 2021

• HIVEVO_reversion

  Repository for the analysis and figures of Valentin Druelle's paper on HIV-1 reversion
  Python 0 1 0 0 Updated Jul 23, 2021

• treetime

  Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

  phylogenetics
  Python MIT 45 107 13 2 Updated Jul 16, 2021

• treetime-cloud
  TypeScript 2 3 0 0 Updated Jun 27, 2021

• 2020_EU1_paper
  Python 0 1 0 0 Updated Jun 3, 2021

• compbio-trial
  0 0 0 0 Updated May 17, 2021

• enterovirus_a71
  Jupyter Notebook 0 1 0 0 Updated May 16, 2021

• SVVC

  simple viral variant caller
  Python MIT 3 4 0 0 Updated May 16, 2021

• ncov-swiss

  Forked from nextstrain/ncov

  Nextstrain build for novel coronavirus SARS-CoV-2
  Python MIT 340 1 0 0 Updated May 13, 2021

• ncov-europe
  Python MIT 2 8 0 1 Updated May 13, 2021

• HIVEVO_recombination

  Scripts created to analyse recombination in HIVEVO dataset
  Jupyter Notebook MIT 1 1 0 0 Updated May 12, 2021

• pan-genome-visualization

  Forked from wdingx/pan-genome-visualization

  Visualization of the pan-genome output by panX
  JavaScript GPL-3.0 17 41 3 1 Updated Apr 16, 2021

• sequence_distances
  Python 1 1 0 0 Updated Feb 17, 2021

• FitnessInference

  Forked from rneher/FitnessInference

  Prediction fitness of leaves on a genealogical tree
  Python MIT 6 3 0 1 Updated Feb 1, 2021

• nextalign Archived

  🧬 Viral genome reference alignment
  MIT 1 10 0 0 Updated Jan 26, 2021

• HIVEVO_access
  Python MIT 5 5 2 0 Updated Dec 15, 2020

• demo-auspice-tree

  Demonstrates how to embed Auspice tree into React application
  JavaScript MIT 1 2 0 0 Updated Sep 25, 2020

• 2019_Puller_SiteSpecificGTR
  TeX 3 2 0 0 Updated Aug 10, 2020

• covid19_scenarios_data Archived

  Data preprocessing scripts and preprocessed data storage for COVID-19 Scenarios project

  open-source science data opensource research simulation model
  Python 38 44 0 0 Updated Apr 1, 2020

• CoV_Seasonality

  Model coronavirus seasonality and explore consequences for nCoV dynamics
  TeX 5 15 0 0 Updated Mar 14, 2020

• EV-D68_sequence_mapping

  Code processing and analyzing data from Dyrdak et al, 2019
  Python MIT 2 2 0 0 Updated Jan 6, 2020

• 2018_evd68_paneurope_analysis

  Scripts producing figures and analysis of Hodcroft et al, 2020
  Python 2 2 0 0 Updated Jan 6, 2020

• pan-genome-analysis

  Processing pipeline for pan-genome visulization and exploration
  Python GPL-3.0 27 84 22 0 Updated Dec 28, 2019

• treetime_web

  Forked from pausag/treetime_web
  JavaScript 3 1 0 0 Updated Sep 2, 2019

• gisaid_nextstrain
  Python 2 2 0 0 Updated Aug 27, 2019

• FluSpeciation

  Code for SIR models with antigenic evolution
  MATLAB GPL-3.0 7 5 0 0 Updated Aug 8, 2019

• 2019_Yan_RQS_flu_analysis
  Python 2 2 0 0 Updated Aug 8, 2019

• treetime_examples

  A collection of documented examples using TreeTime
  Python 12 8 1 0 Updated Jul 30, 2019

• python_morbidostat

  Control software for a morbidostat reactor based on arduino and python
  Python 3 4 0 0 Updated May 22, 2019