Useful PAUP references

This is a working list.

http://paup.csit.fsu.edu/paupfaq/faq.html

http://peter.unmack.net/molecular/programs/paup.command.blocks.html

http://phylo.bio.ku.edu/slides/lab5ML/lab5ML.html

For maximum likelihood estimation, I see several ways to set it up in PAUP.

ML Analysis in PAUP by  Peter Unmack
 

[! Likelihood settings from best-fit model (GTR+I+G) selected by AIC in Modeltest 3.7 on Tue Mar 13 23:03:48 2007]

begin paup;

set criterion=like;

set autoclose=yes;

set root = outgroup;

outgroup fish1 fish2 etc;

set storebrlens=yes;

set increase=auto;

log file=PeterML.log;

Lset  Base=(0.2892 0.2928 0.1309)  Nst=6  Rmat=(3.7285 46.5293 1.3888 2.3793 16.4374)  Rates=gamma  Shape=0.9350  Pinvar=0.5691;

hsearch addseq=random nreps=5 swap=tbr;

savetrees file=datasetname.cb.ml.tree.nex format=altnex brlens=yes maxdecimals=6;

end;