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2018_evd68_paneurope_analysis

Scripts producing figures and analysis of Hodcroft et al, 2020

2019-krisp-nextstrain-workshop

Tutorials, data, and results of the 2019 KRISP nextstrain workshop

2019_puller_sitespecificgtr

2019_yan_rqs_flu_analysis

2020_eu1_paper

allflu

ba286

BA.2.86 project with Sigal lab

betatree

Generate and analyze beta coalescent trees

cluster-mutations

Get mutations in cluster by querying from LAPIS API

compbio-trial

compbio2023

simple viral consensus assembly

cov_seasonality

Model coronavirus seasonality and explore consequences for nCoV dynamics

covid19_scenarios

Models of COVID-19 outbreak trajectories and hospital demand

covid19_scenarios_data

Data preprocessing scripts and preprocessed data storage for COVID-19 Scenarios project

ctlfit

Manuscript: Inferring HIV Escape Rates from Multi-Locus Genotype Data

demo-auspice-tree

Demonstrates how to embed Auspice tree into React application

enterovirus_a71

enterovirus_nextstrain

ev-d68_sequence_mapping

Code processing and analyzing data from Dyrdak et al, 2019

ev_d68_analysis

scripts that generate figures for Dyrdak et al 2018 manuscript

ffpopsim

FFPopSim is a collection of C++ classes and a Python interface for efficient simulation of large populations, in particular when the product of mutation rate and population size is larger than one. It consists of one library for individual-based simulations, and a complementary one for simulation of the entire genotype distribution. The latter is coded efficiently using Fast-Fourier Transforms to speed up recombination operations.

fitnessinference

Prediction fitness of leaves on a genealogical tree

flu-ingest

flu_clades

fluspeciation

Code for SIR models with antigenic evolution

genome-assembly

Bacterial genome assembly pipeline

gisaid_nextstrain

h5nctest

hiv-nextclade

hivevo_access