PAUP 4.0
General information and sample Command blocks.

   Submitting NEXUS files to the CCG Phylocluster


There is only one way to submit a PAUP based analyses to the CCG Phylocluster:


  1. Your NEXUS file must include a PAUP command block.





PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a program for phylogenetic analysis using parsimony, maximum likelihood, and distance methods (Swofford 2003). The program features an extensive selection of analysis options and model choices, and accommodates DNA, RNA, protein and general data types. Among the many strengths of the program are the rich array of options for dealing with phylogenetic trees including importing, combining, comparing, constraining, rooting and testing hypotheses.

You must create a set of PAUP commands (PAUP command block) to perform the analysis of your choice. If your commands include references to subsets of your data, like a set of outgroup OTUs (taxa) or sets of genes (aka partitions) you must include a "Sets" block in your NEXUS file.

Simple Maximum Parsimony analysis

Copy all of the text in the white box below and paste into the end of your NEXUS file after the last "end;" EDIT VALUES TO MATCH YOUR DATA!
begin paup;
  1. log start replace=yes file=FILENAME_log.txt;
  2. set autoclose=yes criterion=parsimony root=outgroup storebrlens=yes increase=auto;
  3. outgroup MyOutgroup;
  4. hsearch addseq=random nreps=1000 swap=tbr hold=1;
  5. savetrees file=mytrees.tre format=altnex brlens=yes;
  6. log stop;

END;


 

Maximum Parsimony Bootstrap analysis


Copy all of the text in the white box below and paste into your NEXUS file after the last "end;" EDIT VALUES TO MATCH YOUR DATA!
begin paup;
  1. log start replace=yes file=FILENAME_log.txt;
  2. set autoclose=yes criterion=parsimony root=outgroup storebrlens=yes increase=auto;
  3. outgroup MyOutgroup;
  4. bootstrap nreps=1000 search=heuristic/ addseq=random nreps=10 swap=tbr hold=1;
  5. savetrees from=1 to=1 file=MyBootTree.tre format=altnex brlens=yes savebootp=NodeLabels MaxDecimals=0;
  6. log stop;

END;




Maximum Likelihood analysis

you must estimate your likelihood models before you create your likelihood command block. We recommend Modeltest 3.7 or MrModeltest2 2.3

Copy all of the text in the white box below and paste into the end of your NEXUS file after the last "end;" EDIT VALUES TO MATCH YOUR DATA!
begin paup;
  1. log start file=MyML_log.txt;
  2. set criterion=distance autoclose=yes storebrlens=yes increase=auto root=outgroup;
  3. outgroup myOutgroups;
  4. DSet distance=JC objective=ME base=equal rates=equal pinv=0 subst=all negbrlen=setzero;
  5. NJ showtree=no breakties=random;

  6. set criterion=like;
  7. 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;
  8. hsearch addseq=random nreps=5 swap=tbr;
  9. savetrees file=MyML_tree.tre format=altnex brlens=yes maxdecimals=6;
  10. log stop;

END;


 

Maximum Likelihood Bootstrap analysis

you must estimate your likelihood models before you create your likelihood command block. We recommend Modeltest 3.7 or MrModeltest2 2.3

Copy all of the text in the white box below and paste into the end of your NEXUS file after the last "end;" EDIT VALUES TO MATCH YOUR DATA!
begin paup;
  1. log start file=MyMLboot_log.txt;
  2. set criterion=like autoclose=yes storebrlens=yes increase=auto root=outgroup;
  3. outgroup myOutgroups;
  4. 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;
  5. bootstrap nreps=1000 search=heuristic/ addseq=random swap=tbr hold=1;
  6. savetrees from=1 to=1 file=MyMLboot_tree.tre format=altnex brlens=yes savebootp=NodeLabels MaxDecimals=0;
  7. log stop;

END;


Related Links

MrModeltest2 explained

PAUP info and commands

MrBayes info and commands

Clustal W info

RAxML info and commands

PAUP Sets blocks