Tuesday, April 29, 2008

PAUP GUI for Mac OSX!

Unbelievable. After years of waiting a GUI interface for the most popular program in phylogenetics - PAUP* - is finally available for Mac OSX on the intel platform! It appeared without fanfare on a page for the CDC's Workshop on Molecular Evolution. Not sure yet how buggy its going to be, but I'm playing with it right now. I can't even remember how to use it; it's been that long.

Updated: Our hopes and dreams must once again be put on hold, the link to the PAUP GUI is gone and the installed version has expired. The link has been updated with a new version for 2009.

13 comments:

Glor said...

Already finding some bugs. I can't get to the "Distance Settings" options (instead I get an error stating that the "Distance settings dialogue is broken"). I also noticed that the following note when I opened the application "This copy is registered to: This version prepared for exclusive use of participants in the CDC Molecular Evolution Workshop. Please do not redistribute." Screw that. I dropped $100 and never even got my PAUP* manual.

Glor said...

Has anybody used the menu-driven frontend for PAUP on Windows (http://www.agro-montpellier.fr/sppe/Recherche/JFM/PaupUp/main.htm)? They claim 80% success with menu commands and full functionality when instructions are submitted via the command line.

sergios-orestis said...

I tried this alpha release, too. Inded, the distance settings don't work yet, the branch&bound search didn't start within the first minute that I stuck around, the ILD test didn't work either. This is all to say I'm looking fwd to an actual release (beta or better). I've tried paupUp and it seems to do most stuff. Note: it doesn't accept spaces in the paths, so it's better to create a directory directly in the C (or whatever) drive, like C:\data, instead of the space-full Windows paths. I haven't done node support via any of the GUIs, mostly because because I don't use PAUP for that stuff anymore. For now, I use it when needed in cmd-line not for tree-building. For everything else, there's RAxML, Garli, and TNT ;)

softLinks | cyclotis

Glor said...

Good stuff Sergio. I haven't done much more poking around, but I am having some annoying problems with innappropriately-sized windows. I'm looking forward to the beta as well, but I stopped holding my breath around four years ago. Funny story: Sinauer still tells you that manual is forthcoming when you purchase PAUP (I bought a new license when I started my lab). As a result, the woman who handles our orders (who's very on top of things) asked me if the PAUP manual had arrived about a month after I placed my order. After a hardy laugh I told her that was something she should cross off her list of things to wait for!

sergios-orestis said...

I'd like to see a beta at some point for education purposes. As for manual, I've done stuff on the cmd-line with the cmd reference. Other than that, I'm super happy with RAxML and TNT for my own research. TreeFinder is ok; some of its methods need to get published, i.e. tested and scrutinized by the community. I had to design computer hands-on for undergrads and I did in Mega4. Simple and easy to use. Just the right thing for ugrads or even early grads.

Nathaniel & Tenille said...

Hi, Just found this thread and am excited to get to play with a "Mactel" menu driven PAUP*. A few questions:

Any more info on what is actually functional in the OSX Intel x86 GUI version? Is this really worth using?

The CDC Windows version: is this a menu driven GUI like PAUP* Classic or just a pseudo-GUI window with a command line?

Windows .zip file seems to be password protected, can't unzip... thoughts?

Any other thoughts on how to scrape together a functional menu driven PAUP* on an Intel Mac?

Glor said...

I haven't tried the Windows version, so I can't be much help there. The Mac version is worth downloading, but you're going to need to supplement with the command line version if you want full-functionality. There is a bit of learning curve, but most of us have become relatively proficient, and many now even prefer it to the GUI version. I'm not really sure what other option you have: history has taught that you shouldn't waste any time waiting for a better GUI.

Glor said...

I should probably go on record in saying that every PAUP user should have a licensed copy, even if you're using the unprotected GUI posted at CDC. The fact that I've given Sinauer/Swofford $100 is the only reason that I personally fell comfortable experimenting with the CDC GUI.

Nathaniel & Tenille said...

Speaking of learning curves I took a look at the PaupUp site and it looked like it outputs commands to the text buffer for any option you execute via the menus. PAUP* does not do this as far as I know. Can anyone verify this? That would seem to help in learning the command line version as well as writing PAUP blocks. I prefer that since I can just submit them to our cluster.

"On record", duly noted and dittoed. Thanks again

Javier said...

Hi everybody, I can´t find the program at the page you mentioned... ¿is it still active?
¿does anyone know other location where I can download it?

Thanks

Glor said...

Sorry Dude, it's gone! Don't worry though, I'm sure the final version will be released sometime before the Sun goes super nova.

jaime said...

just found this page. any chance anyone knows where a licensed owner can find this elusive gem.

Anonymous said...

it's coming...2009 is the year!