The original supertreebase (http://github.com/rvosa/supertreebase) is (amongst other things) a dump of essentially all phylogenetic trees in TreeBASE (treebase.org) in NeXML and other formats, provided by Rutger Vos (http://github.com/rvosa). I have forked it so that I can modify & alter them for testing for the MIAPA-ETL project (http://github.com/miapa/miapa-etl). I'm also trimming out some of the non-XML files for ease of navigation and syncing.
** - IF YOU NEED PHYLOGENETIC DATA PLEASE DO NOT USE THESE FILES - **
Just grab any funky NeXML files you need for testing. Check the commit history to see which trees have been modified.
I don't plan on maintaining this repo, so any real contributions for scripts or other utilities related to using the data for science should be pull requests to rvosa's supertreebase. If you make a gnarly file that's great for testing data conversion utilities then by all means send a pull request my way.
- Elliott December 2012