[Taxacom] running PAUP

Sergio Vargas sevragorgia at gmail.com
Thu Dec 11 16:14:17 CST 2008


A note on CIPRES. If the run takes more than 72 hrs it may be killed!!!

You could also try this cluster:


you need an account and a PAUP license, and the jobs are allowed to run...
and run, and run!

Now... in bioportal.uio.no PAUP doesn't run in parallel. You'll have a
single machine running your analysis until completion. You will also need a
batch file. A matrix of about 600 nucleotides and 80 taxa took about three
weeks to finish using the following "tricks".

Some advice with PAUP, if you are running a bootstrap analysis you may want
to turn the MULTTREES option off, this will speed up the analysis with
little or no impact on the result. Furthermore, you can restrict the number
of rearrangement PAUP does on each replicate. I've seen that the score of
the tree does not change after about 10000 rearrangements, though this is
data-set specific. You may want to check first, using say 2 or 3 reps, how
many rearrangements are ok for your data set, and then limit the number of
rearrangement per replicate. This will considerably speed the analysis.

I am assuming, based on the size of your matrix, you have molecular data. If
so, you could try GARLI for ML. I have access to a small cluster were I
could run your data if you provide the garli batch file (I could though send
you some example). Your matrix should take a couple of days to run, if every
thing goes as expected (we are testing the cluster and GARLI).

If you need a parsimony analysis you could try TNT, which allows more
advance tree search techniques and it is free (as in free bier!). I you
still want to use PAUP you could try PRAP to set a parsimony ratched with

If you send the command lines you are using to set PAUP, may be some could
suggest some better tricks.

good luck.

Sergio Vargas, M.Sc.
Center for Marine and Limnological Research
University of Costa Rica

"Si nos portamos bien, está prometido, veremos las mismas imágenes y
escucharemos los mismos sonidos y vestiremos las mismas ropas y comeremos la
misma chatarra y estaremos solos de la misma soledad dentro de casas iguales
en barrios iguales de ciudades iguales donde respiraremos la misma basura y
serviremos a nuestros automóviles con la misma devoción y responderemos a
las ordenes de las mismas máquinas en un mundo que será maravilloso para
todo lo que no tenga piernas ni patas ni alas ni raíces"

E. Galeano

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