Saturday, December 22, 2007

T(ree analysis using)N(ew)T(echnology) is free

This post at Blind.Scientist alerted me to the fact that TNT is now free, thanks to support from the Willi Hennig society. That's worth repeating here. The Blind.Scientist blog mentions a review is in the works, so check back there shortly. This is a great step forward as TNT has a lot of promise, particularly with respect to its scripting capabilities. Much of that promise is locked up in, if I dare say, its somewhat cryptic help documentation, and buggy script examples. I've worked a lot with TNT in the past, but haven't checked the latest documentation, so take this observation with a grain of salt (a small one). I've mentioned to Pablo, and have heard others comment, that what is needed is a community wiki similar to that supporting Beast (a wonderfully supported piece of software, see the active mailing-list for example). This suggestion has thus far fallen on deaf ears, but maybe now that the software is more accessible (somewhat, it still isn't open source, which is a major strike against it IMO), something will happen. As a side note- I've had problems running the latest TNT on OSX 10.3.9, and Pablo wasn't able to get me a compiled copy that worked. I'd be curious if anybody has similar problems, or whether its just my old PowerBook giving up the ghost.

Friday, December 14, 2007

pixels to Newick

Bioinformatics sports a new paper on an application called TreeSnatcher. The meat of the problem is essentially recognizing and converting a tree in a picture (pixels) to a representation in Newick format. While nifty I'm not sure this is particularly useful, and perhaps its a reflection of the lack of awareness of sites like TreeBase. Older trees are relatively small, and can be rebuilt using Mesquite or other programs. New trees should of course be archived somewhere so that they can be grabbed auto-magically, or, as my shadowy friends put it, "just ask the $%@* author for the trees". Fire up those screen-caps!

Monday, November 26, 2007

Not practical, but pretty.

A nested set representation of a Newick tree loaded into mx (source in 0.1.1379). Even though this isn't the best way to visualize a phylogenetic tree I was happy to just get this far. Now to see if trees can be drawn using only margins of divs and position:relative, with maybe a little opacity: for good measure. Don't hold your breath on that one.

Friday, November 23, 2007

storing phylogenetic trees in mx

Turkey in belly I've sat down to flesh out the storage of phylogenetic trees in mx. Krishna's phylo_tree lexer/parser creates nice Ruby objects of newick formatted trees, all I had to do was incorporate another of his efforts better_nested_set, to translate the parsed tree to a database table, all in all just a couple lines of new code. Visualization is another can of worms. I think I'll likely wait till a nice Rails/Ruby graph (as in trees) generator comes out before attempting this. As a thought experiment its interesting to think about how to display a tree completely in ascii, and not just drawing the branches with _, -, and |, but rather displaying groups of terminals, or labeled internal nodes in some meaningful manner depending on where you are in the tree. Its late, so I envision starting with something like "you are in twisty set of passages all alike" ...

Wednesday, November 21, 2007

Morphbank updated, now with matrices

Morphbank has been updated with new features including the ability to create and score OTUs. They will also be rolling out some new searches that return RDF and XML in the very near future, and functionality for allowing external clients to upload images.

Wednesday, November 7, 2007

relation_browser plugin for Rails

The relation_browser plugin is a neat start at using a SWF plugin written by Moritz Stefaner in a Rails environment. I've implemented it in a crude manner in mx as a taxon name hierarchy browser. I'd like to get it to work with the simple ontology editor/displayer that's also in mx, though I'll likely wait to attempt this untill the plugin is a little more mature. Every once in a while its definitely worthwhile to check out Agile's catalog of Rail's plugins for gems like this.

Tuesday, November 6, 2007


First post, maybe last. The open source visualization toolkit Flare appears at first glance (and second) to have some potential as tool for rendering phylogenetic trees. A quick look at the demo reel should convince you of this, click on the "GraphView" button therein to jump to the trees bit.