Tutorials

Twelve UniProt accessions to an alignment, a tree and Pfam domains, in four commands outside the viewer.

Search six bacterial genomes with an Rfam covariance model, align the 37 hits, and read the consensus structure off the result.

474 human kinase domains, comparing the ATP-pocket residues of the kinases imatinib inhibits with those it does not.

ClinVar, AlphaMissense and a saturation screen, each a bar per residue over the same fifteen-species p53 alignment.

Fourteen vertebrate TDP-43 orthologs, each with the per-residue pLDDT of its own AlphaFold model.

32 TRIM5 orthologs to a codon alignment, a tree, an exon structure and a per-codon dN/dS track from HyPhy.

Eleven coronavirus spikes, the four residues its closest relatives lack, and a SIFTS correspondence recording which residues of that row PDB 6VXX resolved.

Alpha and beta globin from eleven vertebrates, with the residue pairs in contact between the chains of PDB 2HHB drawn as arcs.

The spike and hemoglobin alignments beside PDB 6VXX and 2HHB in Mol*. A residue hovered in either view lights in the other.

A Nextstrain tree of 1,840 RSV genomes, reconstructed to an alignment and colored by clade, country, region and year.

204 genomes from Nextstrain's H5N1 cattle-outbreak build, with host, state and one amino-acid site per segment as strips beside the HA alignment.

46 named TEM alleles from NCBI's Reference Gene Catalog, with each one's phenotype and its residues at the Ambler resistance positions.

Eight mammal mitogenomes from RefSeq as one alignment, with all 37 genes per genome drawn as strand arrows colored by respiratory complex.

Twelve bacterial genomes, 8 kb either side of trpB, drawn as gene arrows beside a tree built from TrpB.

Five SARS-CoV-2 genomes aligned whole, with the recombinant XBB.1 scanned against its two BA.2 parents to place the breakpoint.

Twelve norovirus GII genomes aligned whole, each row colored by its closer parent to place the ORF1/ORF2 breakpoint.

Fourteen peptidase S1 domains from UniProt, aligned with DECIPHER, a tree from ape, and two layers R computes.

25 H3N2 vaccine strains from 1968 to 2022 as one hemagglutinin alignment in Jupyter, with a count of how often each column changed.

The same alignment and tree opened inside JBrowse 2 beside a genome view and an AlphaFold structure, each session a single URL.

The NLRP1 family as an SVG the CLI draws, 6.6 KB gzipped, swapped for the live viewer on a click, measured with Lighthouse against loading the viewer at once.