code: def insert_sequences_into_tree(seqs, moltype, params={},
                                             write_log=True):
      
  
      ih = '_input_as_multiline_string'
  
      raxml_app = Raxml(params=params,
                        InputHandler=ih,
                        WorkingDir=None,
                        SuppressStderr=False,
                        SuppressStdout=False,
                        HALT_EXEC=False)
  
      raxml_result = raxml_app(seqs)
  
      # write a log file
      if write_log:
          log_fp = join(params["-w"],'log_raxml_'+split(get_tmp_filename())[-1])
          log_file=open(log_fp,'w')
          log_file.write(raxml_result['StdOut'].read())
          log_file.close()
  
      '''
      # getting setup since parsimony doesn't output tree..only jplace, however
      # it is currently corrupt
  
      # use guppy to convert json file into a placement tree
      guppy_params={'tog':None}
  
      new_tree=build_tree_from_json_using_params(raxml_result['json'].name, \
                                                 output_dir=params["-w"], \
                                                 params=guppy_params)
      '''
  
      # get tree from 'Result Names'
      new_tree=raxml_result['Result'].readlines()
      filtered_tree=re.sub('\[I\d+\]','',str(new_tree))
      tree = DndParser(filtered_tree, constructor=PhyloNode)
  
      raxml_result.cleanUp()
  
      return tree
docs: Insert sequences into Tree.
  
      aln: an xxx.Alignment object, or data that can be used to build one.
  
      moltype: cogent.core.moltype.MolType object
  
      params: dict of parameters to pass in to the RAxML app controller.
  
      The result will be a tree.