Skip to content

Plot catalogue · Evolution and surveillance

Keep estimates, uncertainty and observations distinct

These views join topology, molecular evolution and time without flattening their different evidence into one colour. Karyon renders supplied results: it does not infer ancestral states, fit codon or coalescent models, smooth lineage frequencies or assert transmission.

6 tree geometries2 temporal tracks1 genomic selection track

Eight synthetic views covering orthogonal, diagonal, curved, circular and unrooted trees, a tanglegram, genomic selection layers, a phylodynamic trajectory and lineage surveillance

Choose the biological question

Orthogonal, diagonal, curved, circular and unrooted phylogenetic geometries Topology × geometryTree shapeChoose row alignment, compact radial context or topology-balanced unrooted space without changing the owned tree.Open guide Curved phylogeny with ancestral state donuts, transition marks, mutation lists and concordance intervals Reconstruction × uncertaintyAncestral evidencePlace posterior state composition on internal nodes and direct mutation or interval evidence on the branch that owns it.Open guide Branch rate mixtures, recurrence links and genomic site-wise selection evidence Branch × codon × genomeMolecular evolutionSeparate fitted rate classes, effect direction, statistical evidence, recurrence and observed genomic variants.Open guide Log-scale effective population trajectory with uncertainty ribbon Time × inferred population processPhylodynamicTrackDraw skyline, effective population, reproductive-number or growth estimates with their interval still visible.Open reference Stacked lineage frequencies with sampling-aware alert markers Time × observed lineage countsSurveillanceTrackCompare lineage composition or trajectories while keeping counts, denominators and alert reasons inspectable.Open reference Core and accessory trees joined through matching taxa Topology × topologyEvolutionary comparisonExpose gene-tree, species-tree, core or accessory disagreement as traceable crossings.Open reference

Data contract

Supplied result Karyon encoding Deliberate boundary
ancestral state probabilities internal-node donuts and confident transition cues no ancestral reconstruction
direct branch events ordered branch symbols and optional recurrence links no event inference or convergence claim
point estimate with bounds branch whisker or temporal uncertainty ribbon no interval estimation
branch or site ω results neutral-centred colour, rate mixtures and separate evidence marks no codon-model fitting
effective size, R or growth through time linear or log trajectory no coalescent or clock fitting
lineage counts and denominators stacked composition or comparable lines no smoothing or extrapolation

Generate the complete synthetic sheet with:

cargo run --example evolutionary_surveillance -- assets

The visual contracts follow the structure of results produced by established upstream workflows: HyPhy methods for molecular selection, Augur ancestral and traits for node and branch reconstruction, Augur frequencies for temporal observations, and TreeTime coalescent models for phylodynamic estimates. Karyon accepts typed values derived from any upstream tool; it does not require or invoke these programs.

Continue with the annotated phylogenetics guide for builders and failure semantics, or open the track API reference for every option.