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jasonsahl/paup_commands.txt Secret

Created March 10, 2015 21:49
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paup_commands.txt
begin paup;
log start file= ST25_simple_parsimony.log;
set autoclose=yes;
set criterion=parsimony;
set storebrlens=yes;
set increase=auto;
hsearch start=stepwise addseq=random nreps=100 swap=TBR;
savetrees file= ST25_simple_parsimony.tre format=altnex brlens=yes;
filter best=yes permdel=yes;
pscores /tl ci ri rc;
describe /diag=yes ;
savetrees file= ST25_simple_parsimony_best.tre brlen=yes from=1 to=500;
describe 1;
log stop;
end
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