Saturday, May 24, 2008

SIMMAP Back On-Line

Stochastic mapping is a method for inferring the position of mutational changes or shifts in morphological or ecological traits on phylogenetic trees. It's a cool method with lots of potentially interesting applications. Although basic stochastic mapping can now be implemented in Mesquite, Jonathan Bollback's program SIMMAP permits one to expand the basic methodology a bit further (one can use SIMMAP, for example, to test character correlations). Unfortunately, this program was removed from its original web-site (the one referenced in Bollback's BMC Bioinformatics application note) and isn't readily accessible via internet searches. Fortunately, he has just provided a link to the program's new page. Check it out. Looks like a new version is on the horizon...

3 comments:

dirtyplants said...

Does anyone know a work-around past the mandatory crashes that happen when you try to import a tree in SIMMAP? This happens on three (OS X 10.4 and 10.5, G4 and Intel) machines in our lab.

Glor said...

I don't think I've had this problem (I just opened a tree on my OSX 10.5 Intel mac running SIMMAP 1.0). What version of SIMMAP are you using and what is the format/source of your input tree? If you feel like sending me your tree I can see if I can get it to open without crashing.

ALG said...

I am having the same problem running Simmap 1.5.2 on my Mac OSX 10.5.8. I tried to email help@simmap.com for suggestions, but the email was bounced back. Any ideas?