code: def make(assembly, samples):
      
  
      ## get the longest name
      longname = max([len(i) for i in assembly.samples.keys()])
      names = [i.name for i in samples]
  
      partitions = makephy(assembly, samples, longname)
      makenex(assembly, names, longname, partitions)
docs: Make phylip and nexus formats. This is hackish since I'm recycling the 
      code whole-hog from pyrad V3. Probably could be good to go back through 
      and clean up the conversion code some time.