1. Casey Dunn
  2. agalma

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Casey Dunn  committed 562af79

raxml now builds bootstrap trees

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  • Parent commits f07d56c
  • Branches issue-43

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File agalma/genetree.py

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 	sequences.""")
 pipe.add_argument('model', short='m', default='PROTGAMMAWAG', help="""
 	Choose a substitution model of evolution for RAxML.""")
-pipe.add_argument('raxml_flags', default=None, help="""
+pipe.add_argument('raxml_flags', default='', help="""
 	Extra parameters to pass to RAxML. Make sure the flags make sense: refer to
 	the RAxML Manual for help.""")
 pipe.add_argument('min_bootstrap', short='b', type=float, default=0, help="""
 
 	raxml_dir = os.path.join(outdir, 'raxml-trees')
 	utils.safe_mkdir(raxml_dir)
+	
+	# Configure raxml to run both bootstraps and ml
+	n_reps = 100
+	seed = 12345
+	raxml_flags = '-f a -N {0} -x {1} '.format(n_reps, seed) + raxml_flags
 
 	for phylip in glob.glob(os.path.join(phylip_dir, '*.phy')):
 		basename = os.path.splitext(os.path.basename(phylip))[0]