Tools

Some of the software resources we have developed are listed below.

A high-performance phylogenetic tree explorer that lets users visualise trees with millions of sequences.

An interactive browser for annotated microbial genomes.

A toolkit for interrogating deep sequencing datasets, highlighting within-host diversity and rare variants across genomes.

Collaborations

We contribute to community efforts to improve the viral genomic sharing landscape.

We are helping to build Pathoplexus, a new platform for sharing viral genome data.

We are major contributors to Loculus, the software underlying Pathoplexus, alongside partners at the University of Basel, ETH Zurich and Swiss TPH.

More tools!

Maps SARS-CoV-2 lineage changes onto an interactive map for rapid geospatial interpretation.

Converts between genomic and protein coordinates, including ORF1ab/ORF1a/ORF1b frames and nsp boundaries for SARS-CoV-2.

Aggregates published phenotypes for malaria parasite genes.

An installable command-line tool that rapidly dates very large phylogenetic trees using scalable stochastic optimisation.

Smaller experiments and niche applications that have proven useful to collaborators, clinicians, and the wider community.

Calculates precise laboratory solution recipes, adjusting for stock concentrations and desired final volumes.

Explores England’s hospital medicine usage data.

Visualises similarities and differences between PANGO lineages.

Estimates the likelihood that a tree branch originated from molnupiravir treatment using nucleotide context patterns.