PAUPRAT:

Morphobank sets these parameters:
testParam.properties
Parameters: 
# of chars = 315
runtime = 1
Number of Iterations = 100; 
% data to permute = 2; 
Branch-swapping algorithm = tbr 

toolId=PAUPRAT
runtime_=1
specify_nchar_=315
ratchet_params_=20
specify_pct_=2
paup_branchalg_=tbr(default),spr,nni

Job is OK, command line is 'pauprat setup.nex && paup -n < paup_commands.txt'