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Logo of Treebase

TreeBASE

TreeBASE, the community repository of published estimates of phylogeny, is an initiative whose history dates back to the early 1990s. In its current iteration it is an open source project implemented in Java 1.5 and released under a BSD license. This is its source code repository. It is organized in a number of subprojects, which are described below. For more high-level documentation about TreeBASE, visit the wiki.

Essential subprojects for TreeBASE v.2

The following are subprojects that jointly comprise the TreeBASE v.2 MVC application. The application is organized as a data Model that persists on a PostgreSQL database via Hibernate, multiple Views (namely, a JSP/HTML GUI, an oai-pmh web service interface, a tree viewing and editing applet, and a news feed), linked together by a Controller API in Java 1.5, which uses the Spring framework.

  • treebase-core - Java 1.5 ORM API to access the underlying relational database based on PostgreSQL
  • treebase-phylowidget - Java 1.5 browser applet for tree viewing and editing
  • treebase-web - Java 1.5 MVC web application for the JSP/HTML GUI
  • treebase_feed - PHP feed with newest studies, to embed in the JSP/HTML GUI
  • oai-pmh_data_provider - additional Java 1.5 MVC functionality for OAI-PMH interface

Additional files in this directory

  • pom.xml - file for maven that operates on treebase-core and treebase-web
  • .gitignore - filters out certain files from being committed to git
  • .travis.yml - intended for setting up continuous integration using Travis, but does nothing
  • LICENSE.txt - the BSD license, which applies to all artefacts in this project
  • BUILDING.md - build instructions for the core artifacts, uses pom.xml
  • DEPLOYING.md - instructions for deploying TreeBASE compiled artifacts on a web server
  • INSTALL.md - installation instructions to bootstrap an application for data loading (deprecated)
  • LOADING.md - instructions for loading data files (nexus+metadata) from TreeBASE v.1 (deprecated)
  • README.md - this file