tune = args['tune']
regime = args['regime']
permutation_strength = args['permutations']
permutation_type = args['class_permuter']
master_tree_generator = args['master']
filepath = args['directory']
if 'TEMPORARY_DIRECTORY' in os.environ:
tmpdir = os.environ['TEMPORARY_DIRECTORY']
else:
tmpdir = args['temp_directory']
indels = args['indels']
ratevar = args['ratevar']
quiet = args['quiet']
gtp_path = args['geodesic']
sim = SeqSim('base')
sim.hky_model(
alpha=3.551,
beta=1,
Afreq=0.31,
Cfreq=0.18,
Gfreq=0.21,
Tfreq=0.3,
)
if indels:
sim.indels()
if ratevar:
sim.rate_variation()
