docs: def add_seqs_to_alignment(seqs, aln, moltype, 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 Clustal app controller.
      """
      #create SequenceCollection object from seqs
      seq_collection = SequenceCollection(seqs,MolType=moltype)
      #Create mapping between abbreviated IDs and full IDs
      seq_int_map, seq_int_keys = seq_collection.getIntMap()
      #Create SequenceCollection from int_map.
      seq_int_map = SequenceCollection(seq_int_map,MolType=moltype)
  
      #create Alignment object from aln
      aln = Alignment(aln,MolType=moltype)
      #Create mapping between abbreviated IDs and full IDs
      aln_int_map, aln_int_keys = aln.getIntMap(prefix='seqn_')
      #Create SequenceCollection from int_map.
      aln_int_map = Alignment(aln_int_map,MolType=moltype)
  
      #Update seq_int_keys with aln_int_keys
      seq_int_keys.update(aln_int_keys)
  
      #Create Mafft app.
      app = Clustalw(InputHandler='_input_as_multiline_string',\
          params=params,
          SuppressStderr=True)
      app.Parameters['-align'].off()
      app.Parameters['-infile'].off()
      app.Parameters['-sequences'].on()
  
      #Add aln_int_map as profile1
      app.Parameters['-profile1'].on(\
          app._tempfile_as_multiline_string(aln_int_map.toFasta()))
  
      #Add seq_int_map as profile2
      app.Parameters['-profile2'].on(\
          app._tempfile_as_multiline_string(seq_int_map.toFasta()))
      #Get results using int_map as input to app
      res = app()
  
      #Get alignment as dict out of results
      alignment = dict(ClustalParser(res['Align'].readlines()))
  
      #Make new dict mapping original IDs
      new_alignment = {}
      for k,v in alignment.items():
          new_alignment[seq_int_keys[k]]=v
      #Create an Alignment object from alignment dict
      new_alignment = Alignment(new_alignment,MolType=moltype)
      #Clean up
      res.cleanUp()
      remove(app.Parameters['-profile1'].Value)
      remove(app.Parameters['-profile2'].Value)
      del(seq_collection,seq_int_map,seq_int_keys,\
          aln,aln_int_map,aln_int_keys,app,res,alignment)
  
      return new_alignment