example.config

#REQUIRED PARAMETERS
treefile_path = example/example.tre #Must be newick or Nexus format, and include branch lengths
number_of_variable_sites = 20
base_genome_name = gi #Should be the label of a tip in your tree
base_genome_path = example/mini_ref.fasta
output_dir = example_out


#parameters of evolutionary model (comma seperated), in order ac, ag, at, cg, ct, gc (gc = 1)
rate_matrix = 1,1,1,1,1,1

#parameters for read simulation
coverage = 20 #either an integer or a file name of a comma delimited file with tip names and coverage

#OPTIONAL PARAMETERS
prefix = sim_ #optional prefix prepended to sequence names, default is using orginal sequence names

#Optional evolutionary model parameters
gamma_shape = 5 #dafault is no rate variation across sites

#parameters for clustering of variable site locations (OPTIONAL)
mutation_clustering = ON
percent_clustered = 0.25 #The percentage of variable sites whose distance to another site is drawn from the clustering distribution
exponential_mean = 125 #Minimum allowed value = 2

#ART Optional parameters (for more fine grained control ART can be run seperately on the mutated genomes found in outdir/fasta_files)
error_model1 = example/ErrprofR1.txt  # If you haven't generated have one of your own using ART, you can use one supplied by ART.
error_model2 = example/ErrprofR2.txt  # Un-comment these lines (delete the first #) to set a non-default error profile
read_length = 150 #maximum value with example error profile is 150, use a default or generate adifferent error profile for longer reads.
fragment_size = 380
stdev_frag_size = 120