id3c-customizations
Extensions of ID3C for the Seattle Flu Study
Updated 21 Feb 2020 by kairstenfay
ncov
Nextstrain build for novel coronavirus (nCoV)
Updated 21 Feb 2020 by emmahodcroft
augur
Pipeline components for real-time phylodynamic analysis
Updated 18 Feb 2020 by jameshadfield
cli
The Nextstrain command-line tool, providing access to Nextstrain components in a local environment with a minimum of fuss.
Updated 18 Feb 2020 by tsibley
id3c
Data logistics system enabling real-time genomic epidemiology. Built for the Seattle Flu Study.
Updated 18 Feb 2020 by tsibley
fauna
RethinkDB database to support real-time virus analysis
Updated 18 Feb 2020 by joverlee521
ncov-phylodynamics
Phylodynamic estimation of nCoV incidence and prevalence
Updated 13 Feb 2020 by trvrb
nextstrain.org
The Nextstrain website
Updated 11 Feb 2020 by jameshadfield
auspice
Web app for visualizing pathogen evolution
Updated 11 Feb 2020 by jameshadfield
mumps-seq
Protocols for sequencing mumps viruses
Updated 16 Jan 2020 by lmoncla
nextflu
Real-time tracking of influenza evolution
Updated 15 Jan 2020 by trvrb
genomic-horizon
Temporal horizons of genomic epidemiology
Updated 30 Dec 2019 by trvrb
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 20 Dec 2019 by evogytis
h5n1-cambodia
Within-host diversity in H5N1-infected humans and poultry in Cambodia
Updated 26 Nov 2019 by lmoncla
phylodynamics-lecture
Lecture on viral phylodynamics
Updated 20 Oct 2019 by trvrb
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 28 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 23 Jul 2019 by trvrb
sismid
Pathogen evolution, selection and immunity
Updated 17 Jul 2019 by sarahCobey
mers-structure
Looking into MERS-CoV dynamics through the structured coalescent lens
Updated 25 Aug 2018 by trvrb
zika-usvi
Evolutionary analysis of USVI Zika epidemic
Updated 10 Aug 2018 by trvrb
roka
Evolutionary and epidemiological analysis of Roka HIV outbreak
Updated 8 Aug 2018 by alliblk
sacra
Cleaning scripts for real-time pathogen analysis
Updated 11 Jun 2018 by trvrb
janus
Build and deploy Nextstrain
Updated 7 Feb 2018 by huddlej
unsampled
Estimating unsampled viral diversity
Updated 23 Aug 2017 by trvrb
siv-cst
Dynamics of cross-species transmission in SIV
Updated 15 Jun 2017 by
mitii
Pathogen evolution, selection and immunity
Updated 24 May 2017 by trvrb
yellow-fever
Evolutionary dynamics of yellow fever virus
Updated 17 Nov 2016 by ebaberga
chikv
Evolutionary dynamics of chikungunya virus
Updated 1 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 25 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