def _generate_tree_log_file(self, tree, alignment, output_tree_file_path,<EOL>output_log_file_path, residue_type, fasttree):
if residue_type==Create._NUCLEOTIDE_PACKAGE_TYPE:<EOL><INDENT>cmd = "<STR_LIT>" %(fasttree, tree, output_log_file_path,<EOL>output_tree_file_path, alignment)<EOL><DEDENT>elif residue_type==Create._PROTEIN_PACKAGE_TYPE:<EOL><INDENT>cmd = "<STR_LIT>" %(fasttree, tree, output_log_file_path,<EOL>output_tree_file_path, alignment)<EOL><DEDENT>extern.run(cmd)<EOL>
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.