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TreeBASE is a repository of phylogenetic information: user-submitted phylogenetic trees and the data matrices used to build them. Authors deposit a study once it is tied to a peer-reviewed publication, and readers can search, download and cite the stored trees and matrices by persistent URI. It holds trees and matrices, not raw sequences; sequences live in archives such as GenBank, which TreeBASE links to by accession.
Facts on this page come from the TreeBASE home page and its submission tutorial, read 2026-11-08.
Definition and scope
TreeBASE describes itself as a repository of phylogenetic information, specifically user-submitted trees and the data used to build them. It accepts species, population and gene trees for any biotic taxa, and it is produced and governed by the Phyloinformatics Research Foundation, Inc. The site reports its holdings as of April 2014: 4,076 publications, 8,233 matrices, 12,817 trees and 104,593 distinct taxa. Those figures are a dated snapshot from the site itself, not a current count.
The searchable record includes journal DOIs, specimen georeferences, GenBank accession numbers, and a mapping of taxon names to uBio and NCBI names. Trees can be found by topology search, and studies, trees and matrices each receive persistent URIs. Data can be downloaded in NEXUS and NeXML formats, and a PhyloWS API is offered for programmatic access.
How TreeBASE is used in practice
Submitting a study
The submission tutorial sets out what a valid deposit looks like. Use the checklist below before you start.
- Format: data must be in NEXUS. The tutorial advises checking the file in Mesquite first.
- Content: each submission needs at least one matrix and at least one tree from an analysis of those matrices, linked to an explicit analysis.
- Publication: the work must be tied to a paper in a peer-reviewed journal, book or similar, with all authors listed.
- Taxon labels: use full taxon names and avoid quotation marks, brackets, parentheses, commas, colons and semicolons in labels.
Status lifecycle and access
A new submission is marked “in progress” and receives a submission number and a referee URL. After the paper is accepted it becomes “ready”; staff then check completeness before the data become public. Per the site’s data policy, material becomes public once it is tied to an in-press or published peer-reviewed article, book, proceedings or thesis. Manuscripts in preparation or under review can be deposited but stay private: only the submitter, editors and reviewers (through a special URL) can see them.
Citing deposited data
The tutorial asks authors to cite the study URI in the paper as the accession number, so readers can retrieve the exact trees and matrices.
TreeBASE compared with sequence archives
| Question | TreeBASE | Sequence archive (GenBank) |
|---|---|---|
| What is stored | Phylogenetic trees and the matrices used to build them | Sequence records, which TreeBASE links to via GenBank accession numbers |
The practical point for a data management plan: a phylogenetic study usually needs both. Sequences go to a sequence archive, and the alignment-based matrices and resulting trees go to TreeBASE, with the GenBank accessions cross-referenced. See data management plan for how repository choices are documented, and persistent identifiers for why stable URIs matter for citation.
Where it matters for labs and research offices
- Deposit timing. Because private deposits are allowed during review, a lab can obtain a submission number and referee URL before acceptance and give reviewers access.
- Software upstream. Trees are usually produced with tools such as IQ-TREE, with alignments prepared in editors like Jalview; the output must then be converted to NEXUS with a linked analysis.
- Interpreting what you download. Concepts such as rooting and clades determine how a retrieved tree should be read.
Common misunderstandings
- “TreeBASE stores sequences.” It links to GenBank accessions; matrices and trees are its core content.
- “I can upload a tree on its own.” The tutorial requires at least one matrix plus a tree from an analysis of it.
- “Deposited data are public immediately.” They stay private until tied to an in-press or published peer-reviewed work.
- “The statistics on the home page are current.” They are stamped April 2014.
Sources
- TreeBASE home page, read 2026-11-08.
- TreeBASE submission tutorial, read 2026-11-08.
