Tools

Software we have written for comparative genomics, all open source and on GitHub. Two of them run in the browser and need no installation.

In the browser

The MGT Explorer viewer: a phylogenetic tree above a UMAP scatter of genomes, with a summary and legend panel to the right.
MGT Explorer — the Genome Atlas

A UMAP manifold of 5,821 chromosome-scale genomes across 19 phyla and 4,454 species, linked to a phylogenetic tree. Lasso a region of the manifold and the tree, summary and table follow the selection. The whole dataset is embedded in the page.

The qtqc landing page, showing the file drop area and adapter-trimming options.
qtqc — sequence QC in the browser

FastQC-style quality reports for FASTQ, FASTQ.GZ and FASTA files: per-base quality, sequence content, GC distribution, read lengths, adapter contamination and duplication, for both short and long reads. Everything is computed locally — files are never uploaded.

Packages

odp — oxford dot plots

Macrosynteny analysis and dot plots for comparing chromosome-scale genomes, including the ancestral linkage group inference used throughout our papers.

egt — evolutionary genome topology

Builds the multi-genome manifold behind the Atlas and renders the linked tree and UMAP viewer as a single self-contained HTML file.

Genome annotations and other data releases are listed with the papers they belong to on the Publications page.