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()
print 'Regime = {0}'.format(regime)
print 'Parameter settings:'
params = '\n '.join([
' K: {0}'.format(K),
'M: {0}'.format(M),
'mk: {0}'.format(mk),
'n: {0}'.format(n),
'tune: {0}'.format(tune),
'permutation type: {0}'.format(permutation_type),
'permutation strength: {0}'.format(permutation_strength),
'master tree generator: {0}'.format(master_tree_generator),
'filepath: {0}'.format(filepath),
'tmpdir: {0}'.format(tmpdir),
'gtp path: {0}'.format(gtp_path),
