The primary data objects in TreeBASE are bibliographic references to published
phylogenetic studies, taxon by character data matrices, and phylogenetic trees
resulting from the analysis of such data matrices. Information is also
available that links data matrices and trees, including types of analyses
performed, software used, etc. Wherever possible, taxon labels are mapped to
uBio's name services and NCBI's taxonomy.
Development of TreeBASE
is hosted at SourceForge. All source code can be downloaded from the
subversion repository at SourceForge under a BSD license.
Documentation on installing and running TreeBASE can be
found at the
TreeBASE has a tiered Java-based architecture using the Hibernate and Spring
frameworks built on a PostgreSQL database. The following schematic illustrates
the content and features of this software stack:
TreeBASE stores alignments, character matrices, and trees used for research
that is published in peer-reviewed journals and books.
Each study has one or more analyses; each analysis has one or more steps;
each step associates matrices and trees with algorithms and software.
Each row of sequence alignments or coded characters has a taxon label that
maps to leaf nodes on associated trees. Trees are hashed to allow topological
Each row in a character matrix can be subdivided into one or more row segments;
each row segment can have associated specimen, tissue, or gene sequence metadata.
Names in the rows of a matrix and in row segment metadata can independently
map to a dictionary of name variants, which maps to a taxonomy. This taxonomy will
be mapped to a classification tree in the next release.