--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/raxml.py	Fri Sep 20 13:25:27 2013 -0400
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+
+import random
+import sys
+import shutil
+import gd_util
+
+################################################################################
+
+if len(sys.argv) != 3:
+    gd_util.die('Usage')
+
+input, output = sys.argv[1:]
+random.seed()
+
+################################################################################
+
+prog = 'raxmlHPC'
+
+args = [ prog ]
+
+## required: -s sequenceFileName -n outputFileName -m substitutionModel
+## we supply -s, -n (they are not allowed from user)
+
+args.append('-s')           # name of the alignment data file in PHYLIP format
+args.append(input)
+
+args.append('-n')           # name of the output file
+args.append('fake')
+
+## default options
+args.append('-m')           # substitutionModel
+args.append('GTRGAMMA')     # GTR + Optimization of substitution rates + GAMMA model of rate
+                            # heterogeneity (alpha parameter will be estimated)
+
+args.append('-N')           # number of alternative runs on distinct starting trees
+args.append(1000)
+
+args.append('-f')           # select algorithm
+args.append('a')            # rapid Bootstrap analysis and search for
+                            # best-scoring ML tree in one program run
+
+args.append('-x')           # integer random seed and turn on rapid bootstrapping
+args.append(random.randint(0,100000000000000))
+
+args.append('-p')           # random seed for parsimony inferences
+args.append(random.randint(0,100000000000000))
+
+gd_util.run_program(prog, args)
+shutil.copy2('RAxML_bipartitions.fake', output)
+sys.exit(0)