Pangolin was developed to implement the dynamic nomenclature of SARS-CoV-2 lineages, known as the Pango nomenclature. It allows a user to assign a SARS-CoV-2 genome sequence the most likely lineage (Pango lineage) to SARS-CoV-2 query sequences.
Pangolin assigns lineages to query sequences as described in Rambaut et al 2020.
Serious constellations of reoccurring phylogenetically-independent origin. A tool for snp-based calling of vairants of concern.
View and interact with the latest global SARS-COV-2 phylogenic tree
Civet is a tool developed with 'real-time' genomics in mind.
Using a background phylogeny, such as the large phylogeny available through the COG-UK infrastructure on CLIMB, civet will generate a report for a set of sequences of interest i.e. an outbreak investigation.
Using a background phylogeny, such as the large phylogeny available through the COG-UK infrastructure on CLIMB, polecat will identify and flag clusters based on various configurable statistics.
A website documenting the Pango nomenclature as well as the policies involved with designating new lineages.
A data dashboard for viewing more information about the various SARS-COV-2 variants
A dashboard giving an overview of SARS-CoV-2 variants and interesting mutations
An interactive dashboard displaying various information about the general spread of Covid-19.
A data visualisation tool for exploring important SARS-CoV-2 variants and mutations
A web application version of the Pangolin Tool
Powerful, interactive tools for exploring virus data. Nextstrain provides a large database of viral genomes and bioinformatics pipelines for phylogenetic analysis, including interactive tree visualisations.
Upload your SARS-CoV-2 sequence (FASTA or VCF file) to find the most similar complete, high-coverage samples from GISAID or from public sequence databases (NCBI Virus / GenBank, COG-UK and the China National Center for Bioinformation), and your sequence's placement in the phylogenetic tree generated by the sarscov2phylo pipeline.
Important, global data repository for SARS-COV-2 genomes as well as for other pathogens
The ENA provides a high quality, downloadable data set of SARS-CoV-2 genomes. ENA data is available as a data source on Galaxy.
COG-UK provides a large number of data sets and bioinformatics tools for SARS-COV-2.