• Stars
    star
    1
  • Language
    Python
  • License
    MIT License
  • Created over 5 years ago
  • Updated over 5 years ago

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

scripts that generate figures for Dyrdak et al 2018 manuscript

More 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

flu-ingest

Python
1
star
52

CompBio2023

simple viral consensus assembly
Python
1
star
53

ctlfit

Manuscript: Inferring HIV Escape Rates from Multi-Locus Genotype Data
TeX
1
star
54

TreeKnit-web

TypeScript
1
star
55

HIVEVO_reservoir

Establishment and stability of the latent HIV-1 DNA reservoir
TeX
1
star
56

HIVEVO_recombination

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