docs: def add_seqs_to_alignment(seqs, aln, params=None):
      """Returns an Alignment object from seqs and existing Alignment.
  
      seqs: a cogent.core.alignment.SequenceCollection object, or data that can
      be used to build one.
  
      aln: a cogent.core.alignment.Alignment object, or data that can be used
      to build one
  
      params: dict of parameters to pass in to the Muscle app controller.
      """
      if not params:
          params = {}
  
      #create SequenceCollection object from seqs
      seqs_collection = SequenceCollection(seqs)
      #Create mapping between abbreviated IDs and full IDs
      seqs_int_map, seqs_int_keys = seqs_collection.getIntMap(prefix='seq_')
      #Create SequenceCollection from int_map.
      seqs_int_map = SequenceCollection(seqs_int_map)
  
      #create SequenceCollection object from aln
      aln_collection = SequenceCollection(aln)
      #Create mapping between abbreviated IDs and full IDs
      aln_int_map, aln_int_keys = aln_collection.getIntMap(prefix='aln_')
      #Create SequenceCollection from int_map.
      aln_int_map = SequenceCollection(aln_int_map)
  
      #set output and profile options
      params.update({'-out':get_tmp_filename(), '-profile':True})
  
      #save seqs to tmp file
      seqs_filename = get_tmp_filename()
      seqs_out = open(seqs_filename,'w')
      seqs_out.write(seqs_int_map.toFasta())
      seqs_out.close()
  
      #save aln to tmp file
      aln_filename = get_tmp_filename()
      aln_out = open(aln_filename, 'w')
      aln_out.write(aln_int_map.toFasta())
      aln_out.close()
  
      #Create Muscle app and get results
      app = Muscle(InputHandler='_input_as_multifile', params=params,
                   WorkingDir=tempfile.gettempdir())
      res = app((aln_filename, seqs_filename))
  
      #Get alignment as dict out of results
      alignment = dict(parse_fasta(res['MuscleOut']))
      #Make new dict mapping original IDs
      new_alignment = {}
      for k,v in alignment.items():
          if k in seqs_int_keys:
              new_alignment[seqs_int_keys[k]] = v
          else:
              new_alignment[aln_int_keys[k]] = v
  
      #Create an Alignment object from alignment dict
      new_alignment = Alignment(new_alignment)
  
      #Clean up
      res.cleanUp()
      del(seqs_collection, seqs_int_map, seqs_int_keys)
      del(aln_collection, aln_int_map, aln_int_keys)
      del(app, res, alignment, params)
      remove(seqs_filename)
      remove(aln_filename)
  
      return new_alignment