augur
Pipeline components for real-time virus analysis
Updated 22 May 2019 by rneher
auspice
Web app for visualizing pathogen evolution
Updated 18 May 2019 by jameshadfield
zika-seq
Pipelines to do MinION sequencing of Zika virus
Updated 14 May 2019 by alliblk
dengue-antigenic-dynamics
Dengue antigenic relationships predict evolutionary dynamics
Updated 6 May 2019 by sidneymbell
fauna
RethinkDB database to support real-time virus analysis
Updated 22 Apr 2019 by barneypotter24
cli
The Nextstrain command-line tool, providing access to Nextstrain components in a local environment with a minimum of fuss.
Updated 26 Mar 2019 by tsibley
h5n1-cambodia
within-host diversity in H5N1-infected humans and poultry in Cambodia
Updated 20 Mar 2019 by lmoncla
genomic-horizon
Temporal horizons of genomic epidemiology
Updated 19 Mar 2019 by evogytis
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 14 Mar 2019 by evogytis
nextflu
Real-time tracking of influenza evolution
Updated 12 Feb 2019 by trvrb
zika-colombia
Genetic analysis of the Zika epidemic in Colombia
Updated 8 Feb 2019 by alliblk
h3n2-reassortment
Rapid spread of a reassortant A/H3N2 virus during the 2017-2018 influenza season
Updated 6 Feb 2019 by trvrb
mumps-seq
Protocols for sequencing mumps viruses
Updated 4 Jan 2019 by lmoncla
phylodynamics-lecture
Lecture on viral phylodynamics
Updated 3 Jan 2019 by trvrb
global-migration
Analysis of global migration patterns of seasonal influenza viruses
Updated 10 Oct 2018 by trvrb
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
sismid
Pathogen evolution, selection and immunity
Updated 25 Jul 2018 by sarahCobey
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