<commit_before>![Logo of Treebase](https://treebase.org/treebase-web/images/TreeBASE.png)

TreeBASE
========

TreeBASE, the community repository of published estimates of phylogeny, is an initiative whose 
[history](https://treebase.org/treebase-web/about.html) 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](https://github.com/TreeBASE/treebase/wiki/Documentation).

### Essential subprojects for TreeBASE v.2

The following are subprojects that jointly comprise the TreeBASE v.2 MVC application of 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 using the Spring framework.

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

### Experiments, non-essential subprojects

The following subprojects are not needed for the web application.

- [treebase-notebook](treebase-notebook) - "Hello World"-level code experiment in Java 1.5
- [treebase-derivatives](treebase-derivatives) - code experiments in Perl that build on the TB2 data model
- [treebase-curation](treebase-curation) - a data repository that was used for migrating data from TB1 to TB2

### Additional files<commit_msg>removed old link to notebook<commit_after>![Logo of Treebase](https://treebase.org/treebase-web/images/TreeBASE.png)

TreeBASE
========

TreeBASE, the community repository of published estimates of phylogeny, is an initiative whose 
[history](https://treebase.org/treebase-web/about.html) 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](https://github.com/TreeBASE/treebase/wiki/Documentation).

### Essential subprojects for TreeBASE v.2

The following are subprojects that jointly comprise the TreeBASE v.2 MVC application of 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 using the Spring framework.

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

### Experiments, non-essential subprojects

The following subprojects are not needed for the web application.

- [treebase-derivatives](treebase-derivatives) - code experiments in Perl that build on the TB2 data model
- [treebase-curation](treebase-curation) - a data repository that was used for migrating data from TB1 to TB2

### Additional files
{'fraction_non_alphanumeric': 0.0839231547017189, 'fraction_numerical': 0.011122345803842264, 'mean_word_length': 4.81057268722467, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 6, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2664280', 'n_tokens_mistral': 1153, 'n_tokens_neox': 1081, 'n_words': 471}