conf.txt

# RepeatEvolition configuration file
# Juan Caballero, ISB 2012
# 
# Format:
# Variable := Value
# number of generations
total_generations := 100
# mutation rate per generation
mutation_rate     := 0.01
# frequency of SNV
snv_freq          := 0.80
# frequency of insertions
ins_freq          := 0.10
# size distribution for insertions, format is SIZE=FREQ, FREQs sum must be 1
ins_dist          := 1=0.8,5=0.1,10=0.1
# frequency of deletions
del_freq          := 0.10
# size distribution for deletions, format is SIZE=FREQ, FREQs sum must be 1
del_dist          := 1=0.8,5=0.1,10=0.1
# expansion probability
prob_expansion    := 0.8
# expansion max limit
max_expansion     := 10
# limits when a sequence cannot expand anymore
dead_threshold    := 0.5
# report every X generations
report_generation := 10