Tools- Epidemiology and evolution

Last updated: 2021 Jun 28
Total row(s): 15
Sub-Categories/Data type
Covidex is an open-source, accurate, and fast machine learning-based tool for real-time genome subtyping. Covidex helps to identify SARS-CoV-2 subtypes or clades that represent clusters among isolates from the global population of a defined species.
Viral subtype classification
Marco Cacciabue, Pablo Aguilera, Maria Ines Gismondi, Oscar Taboga
Covidex: an ultrafast and accurate tool for virus subtyping
Pangolin assigns SARS-CoV-2 genome sequences to global lineages based on a rational and dynamic nomenclature. Thus, Pangolin helps in tracking the distribution patterns of the global SARS-CoV-2 spread.
Phylogenetic assignment, epidemiology
Andrew Rambaut, Edward C. Holmes, Aine O Toole, Verity Hill, John T. McCrone, Christopher Ruis, Louis du Plessis & Oliver G. Pybus
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
Beast uses Bayesian inference for creating the phylogenetic tree. It answers evolutionary questions by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others.
Phylogeography analysis
Remco Bouckaert ,Timothy G. Vaughan,Joelle Barido-Sottani, Sebastian Duchene, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kuhnert, Nicola De Maio, Michael Matschiner, Fabio K. Mendes, Nicola F. Muller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, Alexei J. Drummond
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
Nextstrain is an easy to install web application that helps users to visualize the spread of the pathogenic variant over time in a geographic location.
Phylogenetic lineage tracking
JamesHadfield, Colin Megill, Sidney M Bell, John Huddleston, Barney Potter, Charlton Callender, Pavel Sagulenko, Trevor Bedford, Richard A Neher
Nextstrain: real-time tracking of pathogen evolution
COVIDSIM is a simulation tool, web app for simulation and comparison with epidemiological data. It's a prediction tool based on the model for disease progression, number of cases, etc.
Epidemiology, simulations, Tracking transmission/ vaccination/ mutations
Kristan A. Schneider, Gideon A. Ngwa, Markus Schwehm, Linda Eichner & Martin Eichner
The COVID-19 pandemic preparedness simulation tool: CovidSIM
CoV-GLUE is an online web application for tracking SARS-CoV-2 sequence variations. The reports provide visualizations of phylogenetic classification and highlighting genomic variation with primer mismatches. It also acts as a database of amino acid replacements and coding indels region, observed in sequences from the pandemic.
Sequence mutations/variations analysis, Classification, Primer/probe analysis, epidemiology, evolution
Joshua Singer, Robert Gifford, Matthew Cotten, David Robertson
CoV-GLUE: A Web Application for Tracking SARS-CoV-2 Genomic Variation
PoSeiDon is a pipeline to detect significantly positive selected sites and possible recombination events in an alignment of multiple protein-coding sequences. The significantly positive selected sites are detected based on different models for the full alignment and possible recombination fragments. It finally summarizes the result in the HTML format.
Multiple sequence alignment, Recombination analysis, Phylogeny
Martin Holzer, Manja Marz
PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection
CoVariants provides real-time updates and information about key SARS-CoV-2 variants
SARS-CoV-2 Variants/mutations data, Tracking variants/mutations
Emma B. Hodcroft. (Institute of Social and Preventive Medicine University of Bern, Bern, Switzerland & SIB Swiss Insitute of Bioinformatics, Switzerland)
CoVariants: SARS-CoV-2 Mutations and Variants of Interest.
Covid-Miner is an interactive Data Portal with a user-friendly interface to browse the most prominent lineages and Receptor Binding Domain (RBD) Spike mutations worldwide.
Mutations/Variants data, Geographical distribution
Alice Massacci, Eleonora Sperandio, Lorenzo D’Ambrosio, Mariano Maffei, Fabio Palombo, Luigi Aurisicchio, Gennaro Ciliberto and Matteo Pallocca
Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS‑CoV‑2 Spike protein genetic variants
CoVizu is an open-source web resource that provides two interactive visualizations of GISAID data. It provides a phylogenetic tree reporting the evolutionary relationships among different SARS-CoV-2 lineages.
Phylogeny, Variants, evolution, lineage assignment
Roux-Cil Ferreira, Emmanuel Wong, Kaitlyn Wade, Molly Liu, Laura Muñoz Baena, Gopi Gugan, Abayomi S. Olabode and Art F. Y. Poon, at the Department of Pathology and Laboratory Medicine, Western University, Canada.
CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes
COVID-19 CoV Genetics Browser
The COVID-19 CoV Genetics tool (COVID-19 CG) is a free online resource that tracks virus mutations, lineages, and clades using the virus genomes on the GISAID database present in an area during a specific period.
Lineage assignment, Phylogeny
AlbertTian Chen, KevinAltschuler, ShingHei Zhan, YujiaAlina Chan, BenjaminE Deverman
COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest.
Genomic Signature Analysis
Covid19 genomes platform uses alignment-free approaches, genomic signature analysis to represent the similarity of viral genomes in 2-dimensional space. It helps to visualize the relationship between all viral genomes at once.
Emergence, Evolution
Denis C. Bauer, AidanP. Tay, LaurenceO. W. Wilson, DanielReti, CameronHosking, AlexanderJ. McAuley, ElizabethPharo, ShawnTodd, VickyStevens, MatthewJ. Neave, MaryTachedjian, TrevorW. Drew, SeshadriS. Vasan
Supporting pandemic response using genomics and bioinformatics: A case study on the emergent SARS-CoV-2 outbreak
COVID-19 virus mutation tracker system (CovMT) is a SARS-CoV-2 mutation tracker that tracks mutations in the SARS-CoV-2 genome, especially in the spike protein's receptor-binding domain (RBD) region. It provides virus clades, lineages, and mutation information, with metadata of location, date of sampling, and patient disease severity information, at the continent and country levels.
Mutation tracker, Geographic tracking, Tracking visualization
CovMT: an interactive SARS-CoV-2 mutation tracker, with a focus on critical variants
Spike Protein Mutations Monitoring
A web application build on top on the SARS-CoV-2 protein S database to track the mutation in the S protein.
Mutation tracker
Cavallo, L.; Shaik, A. R.; Oliva, R.
D936Y and Other Mutations in the Fusion Core of the SARS-Cov-2 Spike Protein Heptad Repeat 1 Undermine the post-Fusion Assembly
The COVID19-World online web application is a country-specific tool for visualizing epidemiological surveillance. The web provides data analysis of cover time trends, attack rate, population fatality rate, case fatality rate, and basic reproduction number.
Country-specific epidemiological surveillance
Cristian Tebe, Joan Valls, Pau Satorra & Aurelio Tobias
COVID19-world: a shiny application to perform comprehensive country-specific data visualization for SARS-CoV-2 epidemic