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!