PAUP の使い方

begin paup;

    log start replace=yes file=hsearch_log.txt;

    set autoclose=yes criterion=parsimony storebrlens=yes increase=auto;

    hsearch addseq=random nreps=1000 swap=tbr hold=1;

    savetrees file=mytrees.tre format=altnex brlens=yes;

    contree all / majrule=yes strict=no treefile=Consensustree.tre;

    log stop;

END;

begin paup;

    log start replace=yes file=bootstrap_log.txt;

    set autoclose=yes criterion=parsimony storebrlens=yes increase=auto;

    bootstrap nreps=1000 search=heuristic/ addseq=random nreps=5 swap=tbr hold=1;

    savetrees from=1 to=1 file=BootTree.tre format=altnex brlens=yes savebootp=NodeLabels MaxDecimals=0;

    log stop;

END;

Begin PAUP;

log start = yes file = MyFile.log replace = yes;

set criterion=distance;

Lset base=equal nst=6 rmat=(1.0000 2.5287 1.0000 1.0000 7.1401) rates=gamma shape=0.2080 ncat=4 pinvar=0; Paste best model file here

Bootstrap search = NJ  nreps = 1000 conLevel = 50;

saveTrees from = 1 to=1 file=NJ_boot.tre saveBootP=nodeLabels maxDecimals=1 replace=yes;

end;