Here is a gallery of phylotree examples.


A working example with the minimal amount of coding.


A phylogenetic tree that interfaces with a D3.js bar chart to count classes of substitutions along portions of a phylogeny.


The simplest tree possible, with all default features disabled.

Custom menu items

Adding a custom menu item to italicize node names. Leaf node menus now have an additional option “Italicize node label”.

Radial tree

A tree with a button to toggle a radial layout.

Branch coloring and thickness

Adjust color of branches by membership value and thickness by bootstrap value.

Variable size and shape for leaf nodes

Draw different shapes and sizes for leaf nodes (based on haplotype diversity).


Example of zooming and panning.

Leaf metadata

Visualize some artificial data associated with leaves of a tree.

XML parsing

Parse PhyloXML or NexML formats.

Large tree

Viewing a large tree with a Starcraft-style guide.

Web application

A web application for visualizing and annotating phylogenetic trees. Load trees as files or text, make multiple named selections with a variety of mechanisms, and save annotated trees for further use.

Ancestral sequence structural viewer

Interfacing with PV, the Javascript protein viewer, to visualize ancestral substitutions on a protein structure. HyPhy was used to infer ancestral substitutions on an alignment of hemagglutinin. Users can make two types of branch selections. Any branch that is selected and has inferred non-synonymous substitutions will instantaneously highlight positions where those substitutions occurred on an associated protein structure.

Interactive tanglegram

A tanglegram to compare phylogenies inferred from muliple vs. single tissue samples. Crossings are minimized using a dynamic programming algorithm, and the single-tissue tree enables selections to highlight inter-tree crossings.