MetaPIGA is a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood).
Official release note can be found here: http://www.scribd.com/doc/127358328/MetaPIGA-v3-release-note
Official website: www.metapiga.org
Members of this group do quite well.
Vince Smith has http://www.mendeley.com/profiles/vince-smith/ has 28 readers for
Kate Jones has 26 for http://www.mendeley.com/research/a-phylogenetic-supertree-of-the-bats-mammalia-chiroptera-1/
Both Vince and Kate have yet to claim authorship of these papers on their Mendeley profiles!
In an ideal world, these annotations would be (translatable into) triples such that the subject is the treebase data object's URI, and the predicate, its namespace, and its value are something we agree upon (presumably evolving from the tagging that evolves here).
For example like this:
Where "mug:" binds to some sort of "Mendeley User Group" namespace that explains what "hasDOI" means, and where that definition also makes explicit what scheme/format is used for DOIs.
Then, conceivably, TreeBASE would be able to fetch them, understand them and fold them into its output in the appropriate places (web pages, NeXML files), while making it clear that this is non-curated, user-generated content.
TreeBASE http://www.treebase.org/ is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. This group includes all the publications in TreeBASE as of 2010-12-13, and the aim is to clean up and annotate these publications, including adding missing DOIs and PubMed identifers. TreeBASE study numbers (both TreeBASE I and II) are included as keywords and tags, with the prefix "treebase1:" and "treebase2:", respectively.