A Viewer for Large Phylogenies

Tree Diagram
This is a project to explore techniques for visualizing large phylogenies using the Open Tree of Life (OTOL) as a test data set. The goal is to produce tree diagrams that are interesting and useful to students and specialists of particular taxonomic groups.

In this preliminary viewer, the user can select a taxon name and a minimum rank. A subtree will be drawn with the selected taxon at the subtree root and branches extending to descendant taxa that are not lower in rank than the selected minimum rank. In this version, the query will be aborted if it returns more than 2,500 nodes.

The tree supports zooming. A mouse wheel or equvalent will zoom in and out. Also, double-clcking on an area of the tree diagram that is not a taxon name will zoom into that area. A mouse drag will move the tree diagram sideways. Buttons at the top of the subtree page will move the tree back to the top or to the bottom.

The names on the tree have hyperlinks to external web pages or web searches. The default is to search Wikipedia for the taxon name. The type of external link can be changed by the radio buttons at the top of the subtree page. This includes links back to the OTOL tree or taxonomy. In addition, clicking on the node next to a name in the tree links to the OTOL tree for the name.

A PDF of the subtree is generated by clicking on the 'PDF' button at the upper left of the subtree page. Hyperlinks are avaliable from taxa in the PDF, but in a different manner from the web page. Clicking on the left half of the taxon label (including the rank, if any) will search Wikipedia for the taxon name.

Wikipedia Link


Clicking on the right half of the taxon label will link to a Google image search on the taxon name.

Google Image Search Link


Clicking on the node next to the taxon label will link back to the Open Tree of Life tree entry for the taxon.

OTOL Tree Link


Four databases are available. The 'All organisms' database includes all the data in the synthetic tree released by the Open Tree of Life as version 12.3 on 23 Dec 2019. The 'Seed plants', 'Mammals', and 'Birds' databases are subsets that will query much faster than the entire 'All organisms' database. These three subset database only contain nodes at the genus level and above; they contain no species information.

Most trees are cached the first time a user requests them. Subsequent queries for the same tree will be retrieved from the cache in a fraction of a second. Larger trees from the 'All organisms' database may take 2 or 3 minutes to query the first time. Try smaller trees first.

Click here to see a small sample tree: Families of Magnoliidae

Please send any comments to me (chris@phylogram.org).

–Chris Meacham

Query the Viewer







Below are links for some queries. The corresponding PDF files for these trees are also provided.
All organisms database
Queries PDFs
Subclasses of Eukaryotes

Orders of Eukaryotes

Families of Fungi

Orders of Vertebrates

Families of Vertebrates

Families of Amphibians

Genera of Amphibians

Families of Snakes

Genera of Snakes

Orders of Insects

Families of Insects

Families of Mollusks
domain_Eukaryota_to_subclass.pdf

domain_Eukaryota_to_order.pdf

kingdom_Fungi_to_family.pdf

subphylum_Vertebrata_to_order.pdf

subphylum_Vertebrata_to_family.pdf

class_Amphibia_to_family.pdf

class_Amphibia_to_genus.pdf

infraorder_Serpentes_to_family.pdf

infraorder_Serpentes_to_genus.pdf

class_Insecta_to_order.pdf

class_Insecta_to_family.pdf

phylum_Mollusca_to_family.pdf
Seed Plants database
Queries PDFs
Orders of Spermatophyta (seed plants)

Families of Magnoliopsida (flowering plants)

Orders of eudicotyledons

Orders of asterids

Families of asterids

Families of Asterales

Tribes of Asteraceae

Subtribes of Asteraceae

Genera of Asteraceae

Families of Gymnosperms

Genera of Gymnosperms
division_Spermatophyta_to_order.pdf

class_Magnoliopsida_to_family.pdf

eudicotyledons_to_order.pdf

asterids_to_order.pdf

asterids_to_family.pdf

order_Asterales_to_family.pdf

family_Asteraceae_to_tribe.pdf

family_Asteraceae_to_subtribe.pdf

family_Asteraceae_to_genus.pdf

Acrogymnospermae_to_family.pdf

Acrogymnospermae_to_genus.pdf
Mammals database
Queries PDFs
Orders of Mammalia

Families of Mammalia

Genera of Carnivora

Genera of Primates
class_Mammalia_to_order.pdf

class_Mammalia_to_family.pdf

order_Carnivora_to_genus.pdf

order_Primates_to_genus.pdf
Birds database
Queries PDFs
Families of Aves (birds)

Genera of Passerines Large tree of 2,206 nodes
class_Aves_to_family.pdf

order_Passeriformes_to_genus.pdf