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() print 'Regime = {0}'.format(regime) print 'Parameter settings:' params = '\n '.join([ ' K: {0}'.format(K), 'M: {0}'.format(M),