trellis
Evolutionary simulations of lattice proteins
Updated 31 May 2026 by trvrb
ncov-saltational
Quantifying SARS-CoV-2 saltational events
Updated 29 May 2026 by CecileTK
ncov-usa-mig
SARS-CoV-2 geographic and demographic structure in the USA
Updated 28 May 2026 by abemanian
rt-from-frequency-dynamics
Inferring variant-specific effective reproduction numbers from combined case and sequencing data
Updated 15 May 2026 by marlinfiggins
mpox-la
Mpox phylodynamics in Los Angeles County, USA, 2023-2024
Updated 8 Mar 2026 by miparedes
fitness-flux
Fitness dynamics of SARS-CoV-2 and seasonal influenza H3N2
Updated 2 Mar 2026 by trvrb
evofr
Tools for evolutionary forecasting
Updated 9 Feb 2026 by huddlej
phylogeo-signal
Characterizing the informativeness of pathogen genome sequences
Updated 16 Jan 2026 by CecileTK
esm-selection
Correlating seasonal influenza fitness with ESM predictions
Updated 8 Jan 2026 by Cave42
cytb
Nextstrain build for mammalian cytochrome b
Updated 8 Jan 2026 by trvrb
flu-forecasting-delays
Timely vaccine strain selection and genomic surveillance improve evolutionary forecast accuracy of seasonal influenza A/H3N2
Updated 3 Dec 2025 by huddlej
relative-fitness-mechanisms
Frequency dynamics predict viral fitness, antigenic relationships and epidemic growth
Updated 14 Oct 2025 by marlinfiggins
egg-adaptation
Adaptation of influenza virus to chicken eggs
Updated 10 Sep 2025 by kistlerk
adaptive-evolution
An atlas of continuous adaptive evolution in endemic human viruses
Updated 1 Aug 2025 by trvrb
measurements-panel
Manuscript and data describing joint visualization of influenza serology and phylogeny
Updated 14 May 2025 by huddlej
phylo-kernel-public
Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences
Updated 7 Feb 2025 by CecileTK
pathogen-embed
Create reduced dimension embeddings for pathogen sequences
Updated 2 Dec 2024 by huddlej
cartography
Dimensionality reduction of genetic relationships in influenza and SARS-CoV-2
Updated 20 Nov 2024 by huddlej
ncov-forecasting-fit
Assessing frequency forecasts of SARS-CoV-2 fitness models
Updated 2 Sep 2024 by
mpox-dynamics
Phylodynamics of the 2022 mpox epidemic
Updated 16 May 2024 by miparedes
ncov-orf8
Positive selection for ORF8 knockout in SARS-CoV-2
Updated 22 Mar 2024 by cassiawag
flu-forecasting
Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution
Updated 20 Mar 2024 by huddlej
sismid
Pathogen evolution, selection and immunity
Updated 5 Mar 2024 by trvrb
ncov-king-county
Local-scale phylodynamics of SARS-CoV-2 in King County, WA
Updated 20 Feb 2024 by miparedes
size-genetic-clusters
Reproduction number and transmission heterogeneity estimated from clusters of identical pathogen sequences
Updated 8 Feb 2024 by CecileTK
id3c
Data logistics system enabling real-time pathogen surveillance. Built for the Seattle Flu Study.
Updated 4 Dec 2023 by sallybg
nextflu
Real-time tracking of influenza evolution
Updated 8 Sep 2023 by joverlee521
ncov-wa-phylodynamics
Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State
Updated 24 Aug 2023 by trvrb
siv-cst
Modern-day SIV viral diversity generated by extensive recombination and cross-species transmission
Updated 24 Aug 2023 by trvrb
mumps-wa-phylodynamics
Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State
Updated 24 Aug 2023 by trvrb
mers-structure
MERS-CoV spillover at the camel-human interface
Updated 24 Aug 2023 by trvrb
mumps-seq
Protocols for sequencing mumps viruses
Updated 24 Aug 2023 by trvrb
ncov-cryptic-transmission
Cryptic transmission of SARS-CoV-2 in Washington State
Updated 22 Jun 2023 by trvrb
spatial-tumor-phylodynamics
State-dependent evolutionary models of solid tumor growth
Updated 14 Jan 2023 by mlewinsohn
seasonal-cov-adaptive-evolution
Nextstrain builds for seasonal coronavirus
Updated 2 Aug 2022 by kistlerk
sarscov2-adaptive-evolution
Adaptive evolution of SARS-CoV-2 spike
Updated 6 Apr 2022 by kistlerk
ncov-wa-variant-severity
SARS-CoV-2 variant severity assessed in Washington State
Updated 15 Feb 2022 by miparedes
mitii
Pathogen evolution, selection and immunity
Updated 13 Dec 2021 by trvrb
phylodynamics-lecture
Lecture on viral phylodynamics
Updated 28 Oct 2021 by trvrb
ncov-wa-d614g
Updated 30 Mar 2021 by cassiawag
zika-usvi
Evolutionary analysis of USVI Zika epidemic
Updated 24 Jan 2021 by alliblk
gs541-phylodynamics
Lectures and materials for GS541 Introduction to Computational Molecular Biology
Updated 29 May 2020 by trvrb
ncov-phylodynamics
Phylodynamic estimation of nCoV incidence and prevalence
Updated 14 Feb 2020 by trvrb
genomic-horizon
Temporal horizons of genomic epidemiology
Updated 30 Dec 2019 by trvrb
h5n1-cambodia
Within-host diversity in H5N1-infected humans and poultry in Cambodia
Updated 26 Nov 2019 by lmoncla
h3n2-reassortment
Evolution and spread of a reassortant A/H3N2 virus in the 2017-2018 influenza season
Updated 3 Oct 2019 by barneypotter24
zika-colombia
Genetic analysis of the Zika epidemic in Colombia
Updated 1 Sep 2019 by alliblk
dengue-antigenic-dynamics
Dengue antigenic variation and evolutionary dynamics
Updated 29 Aug 2019 by trvrb
zika-seq
Pipelines to do MinION sequencing of Zika virus
Updated 25 Jul 2019 by barneypotter24
global-migration
Analysis of global migration patterns of seasonal influenza viruses
Updated 24 Jul 2019 by trvrb
roka
Evolutionary and epidemiological analysis of Roka HIV outbreak
Updated 8 Aug 2018 by alliblk
unsampled
Estimating unsampled viral diversity
Updated 23 Aug 2017 by trvrb
yellow-fever
Evolutionary dynamics of yellow fever virus
Updated 17 Nov 2016 by ebaberga
chikv
Evolutionary dynamics of chikungunya virus
Updated 2 Sep 2016 by trvrb
medium-data
Talk on data and visualization
Updated 1 Jul 2016 by trvrb
sctrace
Simulating migration patterns using charged particles
Updated 26 Oct 2015 by trvrb
flutrace
Visualizing influenza global circulation patterns
Updated 25 Oct 2015 by trvrb
PACT
Posterior Analysis of Coalescent Trees
Updated 6 Aug 2015 by trvrb
coaltrace
Simulating genealogies using charged particles
Updated 20 Apr 2015 by trvrb
antigen
Simulating virus evolution and epidemiology
Updated 6 Mar 2015 by trvrb
haplotypes
Visualizing evolution as a network of shared mutations
Updated 25 Jul 2014 by trvrb
ancestry
Tracing coalescent histories
Updated 8 May 2014 by trvrb
stem
Picking influenza stem strains
Updated 21 Dec 2013 by trvrb
dynamics-practical
Inferring spatiotemporal dynamics of the H1N1 influenza pandemic from sequence data
Updated 25 Oct 2013 by trvrb
divergence
Illustration of Darwin's Principle of Divergence
Updated 21 Oct 2013 by trvrb