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Phylogeny and clades

Plots that put a tree beside the evidence: annotated trees in several layouts, two trees face to face, genomic spans painted onto clades, and a tree around a map. karyon draws the tree you give it; it does not infer one.

How to choose

Your question Plot Build it with
What does the tree say, with its support and metadata beside it? Annotated tree TreeTrack, --tree
Where do two trees over the same taxa disagree? Tanglegram TanglegramTrack, --tanglegram with --against
Which clades carry a genomic span, and is it one event? Clade blocks CladeTrack, --clades with --with-tree
Where were the tips sampled? Tree around a map PhyloMap, Rust only

To sort rows of sites, genes, residues or domains by a tree, hand the tree to SnpTrack, MatrixTrack, MsaTrack or DomainTrack with .tree(): their plots are under variation and comparisons.

Plots

  • A dated outbreak tree with branches coloured by country and aligned country and depth columns, beside the same tree with two named clades collapsed into triangles

    Annotated tree A phylogram, cladogram or time tree with metadata aligned to its tips, branches coloured by a trait and clades collapsed without changing the tree.

  • Four radial views of one outbreak tree: a circular time tree with country and depth rings, a 250-degree fan with a collapsed clade, time radiating inwards, and a circular cladogram

    Circular and radial trees The same tree as a full circle, a partial fan or radiating inwards, with metadata as rings; the topology and the order of the tips stay the same.

  • An unrooted tree and a circular cladogram carrying the same four datasets: a country strip, radial depth bars, binary resistance marks and host symbols

    Unrooted trees and datasets An unrooted layout centred on the topology rather than on the root the file happened to use, with strips, bars, binary marks and symbols as datasets.

  • One phylogram drawn rectangular, circular and unrooted, with support values as symbols and labels, mutations written along their branches and a branch-length scale bar

    Support, events and scale bars Support as symbols or labels above a threshold, each branch's own events written along it, and a scale bar in branch-length units.

  • The same phylogram rooted three ways, at the source root, on a checked monophyletic outgroup and at the weighted midpoint, each root marked with a diamond

    Rooting choices Reroot at a node, on an outgroup checked for monophyly or at the midpoint, with the new root marked.

  • Abundance bubbles and host bars on a rectangular tree with a highlighted transmission cluster, ancestral-host donuts and a highlighted sector on a radial tree, and an alignment and domain architectures sorted by the same tree

    Node glyphs and clade highlights Bubbles, pies, donuts or stacked bars on nodes and a band or sector behind a clade; a missing value draws no glyph rather than a zero.

  • Core and accessory genome trees of eight isolates face to face, matching tips joined across the middle, with a header reporting seven crossings reduced to five

    Tanglegram Two trees facing each other with every shared tip joined; untangling rotates clades to remove crossings but never changes either tree.

  • Lineage-defining deletions painted across a SARS-CoV-2 phylogeny, each block spanning the lineages that carry it, with the recurrent one cut out where a lineage between the carriers lacks it

    Clade blocks A genomic span painted across the clade that carries it, with any row inside the span that does not carry it cut out, so a scattered set never passes for a clade.

  • Two circular phylogenies around an orthographic globe: a calendar time tree with one link per reported location, and a partial cladogram with a link from every sample

    Tree around a map A circular tree framing a map, its tips linked to the locations you supply, place by place or sample by sample; nothing about migration is inferred.

  • Evolution and surveillance

    Ancestral states and selection on the same trees, and trajectories and lineage counts through time.

  • Variation and association

    Variable sites and genotype matrices sorted by a tree.

  • Phylogenetics

    Reading trees and their annotations, dates, layouts, rooting and collapsing.

  • Tree viewer

    Open a tree in the browser and explore it, from a handful of tips to a million.