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adaptive-evolution

An atlas of continuous adaptive evolution in endemic human viruses

antibody-response-pulse

Model of cross-reactive antibody response from B cells after infection or vaccination

antigenic-clustering

Detailed antigenic dynamics of influenza virus revealed by Bayesian phylogenetic clustering

atlas-of-viral-adaptation

b-cell-ld

Linkage disequilibrium analysis of B cell sequences

baltic

baltic - adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. This fork will no longer receive updates, so any further development to baltic is going to happen at https://github.com/evogytis/baltic.

beta-cov

One-off nextstrain build for betacoronavirus

blotter

bedford lab research

blotter-deploy

Script to build and deploy Bedford lab website

blotter-hook

Deploy hook for blotter web app

cartography

Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2

chikv

Evolutionary dynamics of chikungunya virus

cholera

coveme-2021

Materials relating to nextstrain tutorial presented at coVEME workshop 2021

demo

Git demo

dengue-antigenic-dynamics

Dengue antigenic variation and evolutionary dynamics

ebola-dates

Imputing sampling dates from sample IDs and sequences

ebola-narrative-ms

egg-passage

Adaptation, epistasis and antigenic impact of egg-culture in influenza

evofr

Tools for evolutionary forecasting

fast-wavenet

Speedy Wavenet generation using dynamic programming :zap:

flu-forecasting

Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution

flu-forecasting-all-lineages

Seasonal influenza forecasting with all A and B lineages

genomic-horizon

Temporal horizons of genomic epidemiology

global-migration

Analysis of global migration patterns of seasonal influenza viruses

h3n2-egg-evol

Wet lab experimental evolution of H3N2 in eggs

h3n2-reassortment

Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season

h5n1-cambodia

Within-host diversity in H5N1-infected humans and poultry in Cambodia

hcc-tumor-evol

Spatial and clonal dynamics of hepatocellular carcinoma

loes-2024-neutralization-nextstrain

Phylogenetic analysis and visualization of H1N1pdm neutralization data from Loes et al. 2024