Traceback (most recent call last): File "<stdin>", line 6, in <module> TypeError: TreeMixin() takes no arguments

抱歉，我之前提供的代码中存在错误。在使用 `TreeMixin` 类时，不需要传入参数。以下是修正后的代码：

import os
from Bio import Phylo

# 定义物种树文件路径
species_tree_file = '/ifs1/User/dengwei/NTF_data/rotted_species_tree/species_tree.treefile'

# 定义基因树文件夹路径和重排序后的基因树保存路径
gene_tree_folder = '/ifs1/User/dengwei/NTF_data/rotted_gene_tree'
recorder_gene_tree_folder = '/ifs1/User/dengwei/NTF_data/recorder_gene_tree'

# 读取物种树
species_tree = Phylo.read(species_tree_file, 'newick')

# 获取物种树的分支顺序
species_order = []
for clade in species_tree.find_clades(order='level'):
    if clade.name:
        species_order.append(clade.name)

# 遍历基因树文件夹中的所有文件
for file_name in os.listdir(gene_tree_folder):
    if file_name.endswith('.treefile'):
        gene_tree_file = os.path.join(gene_tree_folder, file_name)
        gene_tree = Phylo.read(gene_tree_file, 'newick')

        # 根据物种树分支顺序重新排序基因树
        sorted_gene_tree = gene_tree.__class__(gene_tree)
        sorted_gene_clades = []

        for species_name in species_order:
            for clade in gene_tree.find_clades():
                if clade.name and species_name in clade.name:
                    sorted_gene_clades.append(clade)
                    break

        sorted_gene_tree.clade.clades = sorted_gene_clades

        # 保存重排序后的基因树
        recorder_gene_tree_file = os.path.join(recorder_gene_tree_folder, file_name)
        Phylo.write(sorted_gene_tree, recorder_gene_tree_file, 'newick')

        print(f"重排序后的基因树已保存至 {recorder_gene_tree_file}")

请尝试使用修正后的代码，如果还有其他问题，请随时告诉我。