Examples gallery
Click any figure for the code that produces it. Every example simulates with ZOMBI2 and plots with Phylustrator, a separate package — so to run one you need both:
pip install zombi2 phylustrator
Species trees
6Forward birth–death trees — the whole history, survivors and extinctions, with the diversification model made visible.
Yule tree
Pure birth, no extinction — a forward tree of 100 lineages.
pure birth (Yule)
Extinct lineages
The full history behind 50 survivors — their branches solid, extinct lineages dashed.
birth–death
Mass extinction
A pulse at t = 3 culls 75% of lineages — the skyline drops sharply at the dashed line, then recovers.
mass extinction · + skyline
Rate shifts
Speciation runs slow, then fast, then slow — the burst packs branches between the two dashed regime lines.
time-varying birth
Diversity-dependent
Speciation slows as diversity fills up; the skyline rises and plateaus at the cap of 100.
birth–death · + skyline
Shape statistics over many trees
Two thousand trees of 100 tips under each of two processes — diversity-dependence bends the lineage curves over (left), and the γ statistic separates the two sets of trees almost perfectly (right).
simulation study · 4000 treesGenomes
7Genes on chromosomes — a genome as a ring, synteny between genomes, and gene-family events and copy number read against the species tree.
Circular genome (ordered)
A genome as a ring — genes evenly spaced by rank, coloured by family, arrows by strand. plot(g, layout="circular") + genes().
Synteny between two genomes
Two genomes, one per row; ribbons link same-family genes and cross where the order was rearranged. stack([a,b]) + synteny().
Gene-family events on the tree
One family's history on the species tree: duplications (squares), losses (crosses) and transfers (arrows, donor→recipient). plot(tree) + branch_events(…).
Profile copy-number
A family × genome copy-number heatmap, its rows locked to the tips. beside(tree, heatmap(profiles)).
Real genome (Mycoplasma)
A real bacterium — Mycoplasma genitalium, 546 genes at their true base positions, coloured by strand; the forward/reverse switch marks the replication origin. read_gff(…).
An inversion, before → after
One inversion on a circular genome: the affected segment is reversed and its strands flip (the arrows turn round). The band marks the segment in both rings. highlight(g, start, end) + genes().
A transfer highway between clades
Transfers steered to run between two clades (a Clades + Between kernel — topology, not a trait). Tree coloured by clade; the barplot counts transfers by clade pair, so A↔B towers over within-clade.
Sequences
4The dated tree the sequences evolve down, and an alignment lined up row-for-row with its tips.
Sequence phylogram
The clock tree the sequences evolve down — branch lengths are substitutions/site under an uncorrelated relaxed clock, so the tips are not level.
phylustrator · phylogram
Autocorrelated-clock phylogram
The other clock we ship: under the autocorrelated clock the rate drifts parent→child, so related lineages share a rate — branches coloured by lineage rate move in blocks, not salt-and-pepper. substitution = FromParent(spread).
Ancestral sequences at the nodes
A small tree with its internal nodes numbered (0 = initial genome, 1 = crown, …); beside it the reconstructed sequence at each — one free-floating row per node, not aligned to the tips. seqs.ancestral.
Alignment beside the tree
A single-copy family across 20 species, residues coloured (with a nucleotide key), each row locked to its tip. beside(tree, alignment(aln)).
Trait evolution
5A trait evolving down the tree — branches coloured by its value; some paired with a companion panel.
Brownian motion
Free diffusion — sister lineages drift apart with time.
continuous
Ornstein–Uhlenbeck
Pulled to an optimum: a high start (yellow) converges to blue.
continuous
Discrete states
A two-state trait hops between habitats; each branch is painted by its state history.
discrete · Mk
Dependent continuous traits
Two traits evolve together (r = 0.9) — two trees, coloured by each trait, and the tip scatter.
continuous · + scatter
Dependent discrete traits
Two binary characters where one's flip rate depends on the other's state. Two trees, coloured by each character (X green, Y purple), so you can see Y is present where X is; the 2×2 chain (arrow width = rate) is the model. simulate_discrete(states=("00",…), switch={…}).
Conditioning
4Two runs, in order: a trait is grown on the tree and held fixed, then a genome run reads it. The trait's state sets a genome rate, so genome size follows the trait.
Genome reduction
A driver (a trait for the lifestyle) modifies the rate of loss (the target). Endosymbionts also gain genes more slowly, so their genomes shrink. The tree is coloured by the lifestyle and the bars are genome size at each tip.
trait → loss
Genome expansion
A driver (a trait for the strength of selection) modifies the rate of duplication (the target). Under relaxed selection duplicates accumulate and the genomes grow. The tree is coloured by the selection regime and the bars are genome size at each tip.
trait → duplication
HGT uptake by competence
A driver (a trait for competence) modifies who receives a transfer (the target), not a rate. Competent lineages take up DNA more often and their genomes grow. The tree is coloured by competence and the bars are genome size at each tip.
trait → transfer uptake
A continuous driver
A driver (a diffusing continuous trait) modifies the rate of origination (the target). A Curve turns each value into a factor, so genome size follows the trait. The tree is coloured by the trait value and the bars are genome size at each tip.
Joining
3One run makes both. The trait sets the speciation or extinction rate of the lineage carrying it, so the trait and the tree are produced together.
BiSSE
A two-state trait drives speciation — the fast state's clades take over; the inset is the state Markov chain.
trait → speciation
State-dependent extinction
One state dies far faster; the doomed lineages (dashed) drop out.
trait → extinction
MuSSE
Three graded speciation rates with constant death — the fastest state fills the tree, extinct lineages dashed.
trait → speciation