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neherlab

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Top repositories

1

covid19_scenarios

Models of COVID-19 outbreak trajectories and hospital demand
JavaScript
1,361
star
2

treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
Jupyter Notebook
206
star
3

pan-genome-analysis

Processing pipeline for pan-genome visulization and exploration
Python
127
star
4

SARS-CoV-2_variant-reports

Informal summaries of notable SARS-CoV-2 lineages
102
star
5

pangraph

A bioinformatic toolkit to align genome assemblies into pangenome graphs
Julia
75
star
6

covid19_scenarios_data

Data preprocessing scripts and preprocessed data storage for COVID-19 Scenarios project
Python
42
star
7

treetime_examples

A collection of documented examples using TreeTime
Python
15
star
8

CoV_Seasonality

Model coronavirus seasonality and explore consequences for nCoV dynamics
TeX
15
star
9

nextalign

🧬 Viral genome reference alignment
12
star
10

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.
C++
12
star
11

PoissonNMF

ImageJ plugins for blind decomposition of fluorencence microscopy data
Java
11
star
12

ncov-europe

Python
8
star
13

treetime-cloud

TypeScript
6
star
14

HIVEVO_access

Python
5
star
15

python_morbidostat

Control software for a morbidostat reactor based on arduino and python
Python
5
star
16

FluSpeciation

Code for SIR models with antigenic evolution
MATLAB
5
star
17

nextclade_data_workflows

Python
4
star
18

genome-assembly

Bacterial genome assembly pipeline
Python
4
star
19

HIVEVO_figures

Python
4
star
20

HIV_time_of_infection

Estimating time of HIV-1 infection from next-generation sequence diversity (code and data)
Python
3
star
21

SVVC

simple viral variant caller
Python
3
star
22

synmut

Manuscript: Quantifying Selection against Synonymous Mutations in HIV-1 env Evolution.
TeX
3
star
23

2019_Yan_RQS_flu_analysis

Python
3
star
24

gisaid_nextstrain

Python
3
star
25

2019-krisp-nextstrain-workshop

Tutorials, data, and results of the 2019 KRISP nextstrain workshop
Python
3
star
26

timetree_viewer

CSS
3
star
27

HIVEVO_reversion

Repository for the analysis and figures of Valentin Druelle's paper on HIV-1 reversion
Python
3
star
28

treetool

tool to build and visualize annotated influenza phylogenies based on blab/nextflu
CSS
3
star
29

flu_clades

Python
3
star
30

treetime_validation

Python
3
star
31

EV-D68_sequence_mapping

Code processing and analyzing data from Dyrdak et al, 2019
Python
2
star
32

SC2_variant_rates

analyze substitution rate and mutation behavior within variants.
TeX
2
star
33

2019_Puller_SiteSpecificGTR

TeX
2
star
34

2020_EU1_paper

Python
2
star
35

BA286

BA.2.86 project with Sigal lab
Python
2
star
36

demo-auspice-tree

Demonstrates how to embed Auspice tree into React application
JavaScript
2
star
37

ratchet

TeX
2
star
38

allflu

2
star
39

krisp

visualization repository for the 2019 nextstrain workshop at KRISP
2
star
40

spike-only

Spike-only SARS-CoV-2 Nextstrain build
Python
2
star
41

ncov-simple

Python
2
star
42

2018_evd68_paneurope_analysis

Scripts producing figures and analysis of Hodcroft et al, 2020
Python
2
star
43

pid

Manuscript: Challenges with Using Primer IDs to Improve Accuracy of Next Generation Sequencing
Python
1
star
44

nextstrain_base

pipeline components for realtime virus analysis
Python
1
star
45

cluster-mutations

Get mutations in cluster by querying from LAPIS API
Python
1
star
46

enterovirus_nextstrain

Python
1
star
47

sequence_distances

Python
1
star
48

multiflu

interactive flu trees side-by-side
JavaScript
1
star
49

enterovirus_a71

Python
1
star
50

reccoal

Manuscript: Coalescence and genetic diversity in sexual populations under selection
TeX
1
star
51

EV_D68_analysis

scripts that generate figures for Dyrdak et al 2018 manuscript
Python
1
star
52

flu-ingest

Python
1
star
53

CompBio2023

simple viral consensus assembly
Python
1
star
54

ctlfit

Manuscript: Inferring HIV Escape Rates from Multi-Locus Genotype Data
TeX
1
star
55

TreeKnit-web

TypeScript
1
star
56

HIVEVO_reservoir

Establishment and stability of the latent HIV-1 DNA reservoir
TeX
1
star
57

HIVEVO_recombination

Scripts created to analyse recombination in HIVEVO dataset
Jupyter Notebook
1
star