Archaeopteryx.js Phylogenetic Tree Viewer


Archaeopteryx.js provides an interactive display of phylogenetic trees, with the ability to adjust many parameters of the display, download images in multiple formats, and search within the tree.

See also

Accessing Archaeopteryx.js

View icon

Clicking the “VIEW” icon at the top right of the result page of a Gene Tree Service analysis job result will open the Archaeopteryx display.

Archaeopteryx display

Archaeopteryx provides an interactive graphical representation of phylogenetic trees control panels on the left and right side of the tree display. The controls are described below.


The following describes the standard controls (found in the left control box). Depending on the tree displayed, some buttons might not be present. For example, if the tree being shown lacks confidence values (“bootstrap values”), the button to show confidence values does not appear.

Tree Display Types

Tree Display Types

  • P for phylogram display (uses branch length values)

  • A for phylogram display (uses branch length values) with left-aligned labels

  • C for cladogram display (ignores branch length values)

Alternatively, use Alt+P (“Option” on Macintosh) to cycle between these display types.

Display Data

These settings control which data is being shown. In general, only relevant buttons are shown (for example, for a tree which has no internal labels, the “Internal Labels” button is not shown). Depending on the tree being displayed additional buttons might also be present.

Display Data

  • Node Name to show/hide node names (node names usually are the untyped labels found in, for example, New Hampshire/Newick formatted trees)

  • Taxonomy to show/hide node taxonomic information

  • Sequence to show/hide node sequence information

  • Confidence to show/hide confidence values

  • Branch Length to show/hide branch length values

  • Node Events to show speciations and duplications as colored nodes (e.g. speciations green duplications red)

  • Branch Events to show/hide branch events (e.g. mutations)

  • External Labels to show/hide external node labels (e.g. node labels, sequence and taxonomic information – if present)

  • Internal Labels to show/hide internal node labels

  • External Nodes to show external nodes as shapes (usually circles)

  • Internal Nodes to show internal nodes as shapes (usually circles)

  • Node Vis to show/hide node visualizations (node colors, shapes, sizes)

  • Dyna Hide to hide labels depending on expected visibility

  • Short Names to shorten long node labels


These settings control zoom in horizontal and vertical directions. General zoom (where everything changes size) can also be achieved with the mouse-wheel.


  • Y+ to zoom in vertically (Alt+Up or Shift+mousewheel)

  • Y- to zoom out vertically (Alt+Down or Shift+mousewheel)

  • X+ to zoom in horizontally (Alt+Right or Shift+Alt+mousewheel)

  • X- to zoom out horizontally (Alt+Left or Shift+Alt+mousewheel)

  • F to fit the tree to the display size (Alt+C, Alt+Delete, Home, or Esc to re-position controls as well)

  • Alt+plus and Alt+minus to zoom while keeping all font sizes constant

  • Shift+Alt+plus and Shift+Alt+minus or Page Up and Page Down or Shift+Ctrl+mousewheel to change all font sizes


These settings control the tree being displayed.


  • O to “order” the entire tree (Alt+O)

  • R1 to return to super-tree, one branch at the time, if in sub-tree (Alt+R)

  • R to return to complete tree, if in sub-tree

  • U to uncollapse all, if collapse sub-trees present (Alt+U)

  • M to midpoint re-root the tree, if tree is re-rootable (uncollapses as well) (Alt+M)

Node Actions

Node Actions

(Left-) clicking on nodes allows to (not all actions are available at all times):

  • Display Node Data

  • Collapse

  • Uncollapse

  • Uncollapse All

  • Go to Subtree

  • Return to Supertree

  • Swap Descendants

  • Order Subtree

  • Reroot

  • Select/Deselect Node

  • Select/Deselect All Ext Nodes

  • List External Node Data

  • Download Ext Node Data (to download data from external nodes which is currently displayed)

  • Download All Ext Node Data (to download all data from external nodes)

  • List Sequences in Fasta

  • Delete Subtree/External Node

Size Control

These sliders control the size of various elements.

Size Control

  • External label size to control the size of the external label fonts

  • Internal label size to control the size of the internal label fonts

  • Branch label size to control the size of the fonts for confidence and branch lengths

  • Node size to control the size of the external and internal node shapes (if turned on with “External Nodes” and “Internal Nodes”)

  • Branch width to control the branch widths (if not set in the tree itself)



  • Collapse Depth

  • Collapse Feature to collapse nodes based on shared metadata values


The following formats are available for download.


  • PNG image

  • SVG vector image

  • phyloXML tree file

  • Newick tree file


Example: Node fill color representing PANGO lineages:

Visualizations Nodes

Visualizations Settings

The following visualizations are possible (depending on the data present):

  • Label Color to control label colors based on a selected metadata field

  • Node Fill Color to control node colors based on a selected metadata field

  • Node Border Color to control node border colors based on a selected metadata field

  • Node Shape to control node shapes based on a selected metadata field

  • Node Size to adjust node sizes based on the numerical values of a selected metadata field

Vis Legend

  • Show to show/hide legends

  • Dir to toggle between vertical and horizontal alignment of multiple legends

  • Arrows to move the position of legends

  • R to return legends to the default position