# procse mininal parameter file

#aw_len should be set to a guessed upper bound of the length of the sites
aw_len 12
#total_time _steps should be set as high as you can afford to. You can do a test run to see how long 10^6 
#steps take on your system
total_time_steps 1000000.0
#transient_time set to 10% of total_time_steps is reasonable.
transient_time_steps  100000.0
#When clustering N sequences, if the program produces M clusters at the end of annealing, choose at least N*M*2
deep_quench_time_steps 25000.0
#When clustering  N sequences, choose something close to N.
significance_sample_period 50.0

