Make a tree with RAxML.

def build_tree_raxml(self,
                   new_path    = None,
                   seq_type    = 'nucl' or 'prot',
                   num_threads = None,
                   free_cores  = 2,
                   keep_dir    = False):
        """Make a tree with RAxML."""
        # Check output #
        if new_path is None: new_path = self.prefix_path + '.tree'
        # What model to choose #
        if seq_type == 'nucl': model = "GTRGAMMA"
        if seq_type == 'prot': model = "PROTGAMMAJTTF"
        # Threads #
        if num_threads is None: num_threads = multiprocessing.cpu_count() - free_cores
        else:                   num_threads = int(num_threads) - free_cores
        num_threads = max(1, num_threads)
        # Run it #
        temp_dir = new_temp_dir()
        sh.raxml811('-m', model, "-T", num_threads, '-p', 1, '-s', self.path, '-n', 'tree', '-w', temp_dir, '-f', 'a', '-x', 1, '-N', 'autoMR')
        # Move into place #
        if keep_dir:
            shutil.rmtree(new_path)
            shutil.move(temp_dir, new_path)
        if not keep_dir:
            shutil.move(temp_dir + 'RAxML_bestTree.tree', new_path)
        # Return #
        return FilePath(new_path)