I've updated the BLAST a sequence and get a tree tool described in a previous post to output additional details, such as a list of the sequences used to build the tree and some basic metadata (such as the taxon name, name of any associated host, publication, and geographic coordinates). If the sequences are geotagged, then you will also see a little map showing the localities.
One of the things I find frustrating about TreeBASE is that there's no easy way to get an overview of what it contains. What is it's taxonomic coverage like? Is it dominated by plants and fungi, or are there lots of animal trees as well? Are the obvious gaps in our phylogenetic knowledge, or do the phylogenies it contains pretty much span the tree of life?
For this weeks sessions of my phyloinformatics course I'm developing some phylogeny tools. The first is a simple AJAX-based BLAST tool.
As part of a postgraduate course here at the University of Glasgow I'm teaching five sessions on "phyloinformatics", which I've decided to define broadly enough to encompass most of biodiversity informatics. Given that this module is being developed on the fly, and will make use of lots of little "toys" I've developed and discussed on this blog, I've decided to put the course notes online, along with the interactive demos and the source code.
Slides from the recent Phyloinformatics workshop in Edinburgh are now online at the e-Science Institute. In case the e-Science Institute site disappears I've posted the slides on slideshare. | View | Upload your own Heiko Schmidt has also posted some photos of the proceedings, demonstrating how distraught the particpants were that I couldn't make it.
Argh!!! The phyloinformatics workshop at Edinburgh's eScience Centre is underway (program of talks available here as an iCalendar file), and I'm stranded in Germany for personal reasons I won't bore readers with. The best and brightest gather less than an hour from my home town to talk about one of my favourite subjects, and I can't be there. Talk about frustration!