Discover blab/ncov-phylodynamics Open Source project

blotter

bedford lab research

rt-from-frequency-dynamics

One-off nextstrain build for betacoronavirus

beta-cov

Analysis of global migration patterns of seasonal influenza viruses

global-migration

Pipelines to do MinION sequencing of Zika virus

zika-seq

ncov-wa-d614g

sarscov2-adaptive-evolution

Nextstrain build targeted to Omicron

ncov-omicron

Dengue antigenic variation and evolutionary dynamics

dengue-antigenic-dynamics

Nextstrain builds for seasonal coronavirus

seasonal-cov-adaptive-evolution

MERS-CoV spillover at the camel-human interface

mers-structure

Detailed antigenic dynamics of influenza virus revealed by Bayesian phylogenetic clustering

antigenic-clustering

PostScript

size-genetic-clusters

Code and data for "Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences"

siv-cst

Modern-day SIV viral diversity generated by extensive recombination and cross-species transmission

Within-host diversity in H5N1-infected humans and poultry in Cambodia

h5n1-cambodia

Associated analyses for "State-dependent evolutionary models reveal modes of solid tumor growth"

spatial-tumor-phylodynamics

flu-forecasting

Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution

Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2

cartography

Workshop for VEME 2022: Real-time tracking of pathogen evolution using Nextstrain

veme-2022

evofr

Tools for evolutionary forecasting

Analysis of stabilizing and destabilizing mutations in influenza evolution

stability

JavaScript

ncov-variant-rt

Analysis of state-by-variant Rt estimates

markov-intermediate

Calculation of state-distributions along Markov chain

An atlas of continuous adaptive evolution in endemic human viruses

adaptive-evolution

Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State

mumps-wa-phylodynamics

Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season

h3n2-reassortment

Nextstrain build to examine early outbreak of SARS-CoV-2 in Wuhan

ncov-early-outbreak

Nextstrain builds for particular variants of interest

ncov-variants

Spatial and clonal dynamics of hepatocellular carcinoma

hcc-tumor-evol

Cryptic transmission of SARS-CoV-2 in Washington State

ncov-cryptic-transmission

Evolutionary analysis of USVI Zika epidemic

zika-usvi

Genetic analysis of the Zika epidemic in Colombia

zika-colombia

Temporal horizons of genomic epidemiology

genomic-horizon

rsv_adaptive_evo

Protocols for sequencing mumps viruses

mumps-seq

ebola-narrative-ms

Imputing sampling dates from sample IDs and sequences

ebola-dates

Estimating unsampled viral diversity

unsampled

Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

ncov-wa-phylodynamics

MATLAB

popcast

Long-term forecasts for pathogen populations

Materials relating to nextstrain tutorial presented at coVEME workshop 2021

coveme-2021

roka

Evolutionary and epidemiological analysis of Roka HIV outbreak

Comparing fitness dynamics across SARS-CoV-2, influenza H3 and influenza H1

fitness-dynamics

Nextstrain analysis of Norovirus

ncov-usa-mig

norovirus

Augur build for Washington SARS-CoV-2 sequences.

ncov-wa-build

Create reduced dimension embeddings for pathogen sequences

pathogen-embed

Correlating within-host and between-host fitness in SARS-CoV-2

sars2-within-host-selection

Assessing accuracy of fitness model forecasts

ncov-forecasting-fit

cholera

A timeline of your Snakemake run generated from the --stats output.

snakemake-stats

atlas-of-viral-adaptation