Watch viral evolution through sequence mutation, phylogeography, host transmission, and custom CTMC design.
Designed for the beastx site
This standalone prototype now follows the same scientific palette, serif-led hierarchy, and calm card-based interface as the documentation website you want to integrate into.
Fine-tune tree geometry, panel placement, and rate ceilings without leaving the main view.
Node position offsets
Adjust how the tree is staged on the canvas, then reset everything with one click if you want to return to the default composition.
Tree zoom
1.00×
Root
0
0
Internal node
0
0
Tip 1
0
0
Tip 2
0
0
Tip 3
0
0
Panel size and location
Phylogenetics (CTMC panel)
0
0
1.00×
Phylogeography (map panel)
0
0
1.00×
Host transmission (panel)
0
0
1.00×
CTMC maximum rates
Mutation Rate (Phylogenetics)
10
Diffusion Rate (Phylogeography)
10
Transmission Rate (Host)
10
Phylogenetics
5.00
Phylogeography
2.00
Host transmission
2.00
Custom substitution model
1.80
Personalized CTMC editor
Define states, colors, and substitution dynamics for a saved model.
Diagonal cells stay zero. Each row is normalized automatically over the off-diagonal entries when the model is saved.
Phylogenetics: Understanding Sequence Evolution
What is a Sequence?
A sequence is a string of nucleotides (the building blocks of DNA). In this
visualization, each sequence consists of 5 nucleotides, which can be A (Adenine), T (Thymine), G
(Guanine), or C (Cytosine). These are shown as colored boxes along the tree.
What is a Site?
A site refers to a specific position within the sequence. For example, in a
5-nucleotide sequence, there are 5 sites (positions 1 through 5). Each site can independently mutate
to a different nucleotide over time.
How Evolution Works Along the Tree
The phylogenetic tree shows evolutionary relationships. Starting from the root (the
common ancestor), sequences split at internal nodes and evolve independently along
each branch. As sequences travel along branches, they accumulate
mutations—individual nucleotides randomly change to other nucleotides.
The CTMC Figure
The Continuous-Time Markov Chain (CTMC) diagram in the top-left shows the mutation
process. The four corners represent the four possible nucleotides (A, T, G, C). The arrows between
them indicate that any nucleotide can mutate to any other nucleotide over time. The black ring
tracks the first nucleotide of the sequence traveling from Root to Tip 1, showing how it changes
states (mutates) as it evolves.
The mutation rate slider controls how frequently these changes occur during the
animation.
Phylogeography: Geographic Evolution
What is Phylogeography?
Phylogeography combines phylogenetics (evolutionary relationships) with geography
(spatial locations). It tracks how organisms or pathogens spread across different geographic regions
over evolutionary time.
How Geographic Locations Change
Just as nucleotides mutate along the tree, the geographic location of each lineage
also changes. The visualization uses a CTMC model where sequences can "jump" between continents
(North America, South America, Europe, Africa, Middle East, East Asia, and Australia) as they
evolve.
The Map Display
The world map in the top-right shows the current geographic distribution of
sequences. Colored dots represent the current location of each evolving sequence, and the
comet trails show the path taken across the globe.
Understanding the Options
Diffusion Rate: Controls how frequently geographic jumps occur between continents.
All branches: When enabled, shows all three lineages on the map (color-coded: red,
yellow, orange). When disabled, shows only the main tracked lineage (Root → Tip 1).
Sticky paths: When enabled, geographic trails remain permanently visible. When
disabled, they gradually fade over time.
Draw locations: When enabled, shows continent silhouettes behind sequences. When
disabled, shows continent names as simple text.
Host Transmission: Cross-Species Jumps
What is Host Transmission?
Host transmission (also called host-switching or spillover) occurs when a pathogen
jumps from one host species to another. This is a critical process in disease emergence—many viral
diseases affecting humans originated in animal hosts.
How Viruses Jump Between Hosts
Similar to geographic diffusion, the visualization models host transmission as a CTMC process.
Viruses can jump between five different host species: Human, Monkey, Bat, Pig, and
Mosquito. Each jump represents a transmission event where the virus successfully
infects a new host species.
The Host Transmission Panel
The circular panel in the middle-right shows all five host species arranged in a ring. The
colored viruses move between hosts over time, with dashed lines showing active
transmission events. The virus icons are color-coded to match the evolutionary lineages (red,
yellow, orange).
Real-World Examples
Many important diseases have emerged through host transmission: COVID-19 (bat → human), influenza
(birds/pigs → human), Ebola (bat → human), and dengue fever (mosquito → human). This visualization
demonstrates how pathogens can switch hosts as they evolve along the phylogenetic tree.
Understanding the Options
Transmission Rate: Controls how frequently host-switching events occur.
All branches: When enabled, shows viruses from all three lineages. When disabled,
shows only the main tracked lineage (Root → Tip 1).