def _generate_tree_log_file(self, tree, alignment, output_tree_file_path,
                               output_log_file_path, residue_type, fasttree):
        '''Generate the FastTree log file given a tree and the alignment that
        made that tree

        Returns
        -------
        Nothing. The log file as parameter is written as the log file.
        '''
        if residue_type==Create._NUCLEOTIDE_PACKAGE_TYPE:
            cmd = "%s -quiet -gtr -nt -nome -mllen -intree '%s' -log %s -out %s %s" %\
                                       (fasttree, tree, output_log_file_path,
                                        output_tree_file_path, alignment)
        elif residue_type==Create._PROTEIN_PACKAGE_TYPE:
            cmd = "%s -quiet -nome -mllen -intree '%s' -log %s -out %s %s" %\
                                       (fasttree, tree, output_log_file_path,
                                        output_tree_file_path, alignment)
        extern.run(cmd)
Generate the FastTree log file given a tree and the alignment that
        made that tree

        Returns
        -------
        Nothing. The log file as parameter is written as the log file.