bedford lab
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projects
team
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