augur
Pipeline components for real-time phylodynamic analysis
Updated 31 Mar 2023 by victorlin
nextstrain.org
The Nextstrain website
Updated 31 Mar 2023 by victorlin
fauna
RethinkDB database to support real-time virus analysis
Updated 30 Mar 2023 by joverlee521
id3c-customizations
Extensions of ID3C for the Seattle Flu Study
Updated 27 Mar 2023 by bencap
cli
The Nextstrain command-line interface (CLI)—a program called nextstrain—which aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch.
Updated 24 Mar 2023 by tsibley
auspice
Web app for visualizing pathogen evolution
Updated 21 Mar 2023 by jameshadfield
ncov
Nextstrain build for novel coronavirus SARS-CoV-2
Updated 16 Mar 2023 by huddlej
id3c
Data logistics system enabling real-time pathogen surveillance. Built for the Seattle Flu Study.
Updated 13 Mar 2023 by bencap
baltic
baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).
Updated 27 Feb 2023 by evogytis
flu-forecasting
Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution
Updated 25 Jan 2023 by huddlej
mumps-wa-phylodynamics
Public repository for genomic epidemiology investigation of the 2016/2017 mumps outbreak in Washington state
Updated 11 Jan 2023 by lmoncla
nextflu
Real-time tracking of influenza evolution
Updated 10 Jan 2023 by joverlee521
seasonal-cov-adaptive-evolution
Nextstrain builds for seasonal coronavirus
Updated 2 Aug 2022 by kkistler
sismid
Pathogen evolution, selection and immunity
Updated 15 Jul 2022 by sarahCobey
sacra
Cleaning scripts for real-time pathogen analysis
Updated 11 May 2022 by victorlin
mitii
Pathogen evolution, selection and immunity
Updated 13 Dec 2021 by trvrb
phylodynamics-lecture
Lecture on viral phylodynamics
Updated 28 Oct 2021 by trvrb
mumps-seq
Protocols for sequencing mumps viruses
Updated 14 Aug 2021 by lmoncla
ncov-wa-phylodynamics
Analyses of the hCoV-19 outbreak in Washington State
Updated 16 Apr 2021 by nicfel
ncov-wa-d614g
Updated 30 Mar 2021 by cassiawag
zika-usvi
Evolutionary analysis of USVI Zika epidemic
Updated 24 Jan 2021 by alliblk
ncov-cryptic-transmission
Cryptic transmission of SARS-CoV-2 in Washington State
Updated 8 Sep 2020 by trvrb
gs541-phylodynamics
Lectures and materials for GS541 Introduction to Computational Molecular Biology
Updated 29 May 2020 by trvrb
janus
Build and deploy Nextstrain
Updated 6 Apr 2020 by huddlej
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 rapid spread of a reassortant A(H3N2) virus that predominated 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
mers-structure
Looking into MERS-CoV dynamics through the structured coalescent lens
Updated 25 Aug 2018 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
siv-cst
Dynamics of cross-species transmission in SIV
Updated 16 Jun 2017 by
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
infectious-pulse
Many-strain SIR epidemiological model
Updated 31 Dec 2015 by alvason
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