neherlab's repositories
covid19_scenarios
Models of COVID-19 outbreak trajectories and hospital demand
covid19_scenarios_data
Data preprocessing scripts and preprocessed data storage for COVID-19 Scenarios project
CoV_Seasonality
Model coronavirus seasonality and explore consequences for nCoV dynamics
treetime_examples
A collection of documented examples using TreeTime
FluSpeciation
Code for SIR models with antigenic evolution
genome-assembly
Bacterial genome assembly pipeline
python_morbidostat
Control software for a morbidostat reactor based on arduino and python
FitnessInference
Prediction fitness of leaves on a genealogical tree
HIVEVO_reversion
Repository for the analysis and figures of Valentin Druelle's paper on HIV-1 reversion
2018_evd68_paneurope_analysis
Scripts producing figures and analysis of Hodcroft et al, 2020
demo-auspice-tree
Demonstrates how to embed Auspice tree into React application
EV-D68_sequence_mapping
Code processing and analyzing data from Dyrdak et al, 2019
cluster-mutations
Get mutations in cluster by querying from LAPIS API
HIVEVO_recombination
Scripts created to analyse recombination in HIVEVO dataset
ncov-swiss
Nextstrain build for novel coronavirus SARS-CoV-2
nextclade-prereleases
Temp storage for files