neherlab

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

nextalign

🧬 Viral genome reference alignment

ncov-europe

treetime-cloud

HIVEVO_access

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

2019_Yan_RQS_flu_analysis

FitnessInference

Prediction fitness of leaves on a genealogical tree

gisaid_nextstrain

HIVEVO_reversion

Repository for the analysis and figures of Valentin Druelle's paper on HIV-1 reversion

SVVC

simple viral variant caller

2018_evd68_paneurope_analysis

Scripts producing figures and analysis of Hodcroft et al, 2020

2019_Puller_SiteSpecificGTR

2020_EU1_paper

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

enterovirus_a71

HIVEVO_recombination

Scripts created to analyse recombination in HIVEVO dataset

ncov-swiss

Nextstrain build for novel coronavirus SARS-CoV-2

sequence_distances

treetime_web

compbio-trial

nextclade-prereleases

Temp storage for files

SARS2_RBD_Ab_escape_maps