The kind people at Nature have taken pity on my rapidly fading research career, and have highlighted my note "Towards a Taxonomically Intelligent Phylogenetic Database" in Nature Precedings (doi:10.1038/npre.2007.1028.1) on the Nature web site. Frankly this is probably the only way I'll be getting into Nature ...

Here is a live demo of Pygmybrowse using the Catalogue of Life classification of animals provided by GBIF. It's embedded in this post in an tag, so you can play with it. Just click on a node. Taxa in bold have ten or more children, the numbers of children are displayed in parentheses "()". Each subtree is fetched on the fly from GBIF.

As yet another example of avoiding what I should really be doing, a quick note about a reworked version of PygmyBrowse (see earlier posts here and here). Last September I put together a working demo written in PHP. I've now rewritten it entirely in Javascript, apart from PHP script that returns information about a node in a classification. For example, this link returns details about the Animalia in ITIS. You can view the new version live.

While using iSpecies to explore some names (e.g., Sooglossus sechellensis in the Frost et al. amphibian tree mentioned in the last post, I stumbled across two papers that both described a new genus of frog for the same two taxa in the Seychelles. The papers (doi:10.1111/j.1095-8312.2007.00800.x and www.connotea.org/uri/6567cfd7531a77588ee62d78e7b4359b) were published within a couple of months of each other.

I've tidied up the big phylogeny viewer mentioned earlier, and added a simple web form for anybody interested to upload a NEXUS or Newick tree and have a play. Examples: Ants from TreeBASE trichodectid lice from TreeBASE Bats from TreeBASE Frost et al amphibian tree To create your own tree viewer, simply go to http://linnaeus.zoology.gla.ac.uk/~rpage/bigtrees/tv2/ and upload a tree.

The first pPod workshop happened last month at NESCent, and some of the presentations are online on the pPod Wiki. Although I'm a "consultant" I couldn't be there, which is a pity because it looks to have been an interesting meeting. When pPod was first announced I blogged some of my own thoughts on phylogenetics databases.

The latest version of the David and Wayne Maddison's Cartographer module for their program Mesquite can export KML files for Google Earth. They graciously acknowledge my crude efforts in this direction, and Bill Piel's work -- he really started this whole thing rolling. So, those of you inspired to try your hand at Google Earth trees, and who were frustrated by the lack of tools should grab a copy of Mesquite and take it for a spin.

Quick note to say how much fun it is to use Parallels Desktop. It's a great advantage to have Windows XP and Fedora Core 7 running on my Mac. As much as I dislike Internet Explorer, it caught some bugs in my code. It's always useful to try different environments when debugging code, either stand alone or for the Web.

Nature precedings is pre-publication server launched by Nature a few months ago. To quote from the website: Unable to resist, I've uploaded three manuscripts previously languishing as "Technical Reports" on my old server. The three I uploaded now have bright shiny DOIs, which may take a little while to register with CrossRef.

In an earlier post I described the TBMap database (doi:10.1186/1471-2105-8-158), which contains a mapping of TreeBASE taxon names onto names in other databases. While this is one step towards making it easier to query TreeBASE, what I'd really like is to link the data in TreeBASE to sources such as GenBank and specimen databases.

Alexis Stamatakis and Jacques Rougemont have released RAxML BlackBox, a prototype Web-Server for RAxML which is attached to a 200 CPU-cluster located at the Vital-IT unit of the Swiss Institute of Bioinformatics. You can upload your data and the cluster will mul it over for up to 24 hours, so typically you can analyse alignments up to 1,000 to 1,500 sequences at present.