mutation model: 4 gamma categories with alpha = 0.5, closes #7

bin/mkconfig.py

@@ -3,7 +3,7 @@
 """
 Read a PHYLIP-format file and produce an appropriate config file for passing to `dnaml`.
 
-`dnaml` is an rather old program that doesn't play very well in a
+`dnaml` is a rather old program that doesn't play very well in a
 pipeline.  It prompts the user for configuration information and reads
 responses from stdin.  The config file generated by this script is
 meant to mimic the responses to the expected prompts.
@@ -72,8 +72,11 @@ def existing_file(fname):
         print("{}".format(naive))		# naive index in phylip
     else:
         warn("No naïve sequence found!")
+    print("R") # gamma
     print("5")						# Reconstruct hypothetical sequences
     print("Y")						# accept these
+    print("1.41421356237") # CV = sqrt(2) (alpha = .5)
+    print("4") # 4 catagories
 
 
 if __name__ == "__main__":