Error in write.tree(rooted_tree, file = output_file, format = "newick") : unused argument (format = "newick")

抱歉，出现了一个错误。在`write.tree`函数中，没有`format`参数可用。要解决这个问题，你可以将`write.tree`函数的调用更改为`write.tree(rooted_tree, file = output_file)`，这样就可以正确保存有根树了。以下是修改后的代码：

library(ape)

# 设置文件路径
input_dir <- "/ifs1/User/dengwei/NTF_data/7.14/recorder_gene_tree"
output_dir <- "/ifs1/User/dengwei/NTF_data/7.14/rooted_gene_tree"

# 获取所有基因树文件的列表
gene_tree_files <- list.files(input_dir, pattern = "\\.tre$", full.names = TRUE)

# 循环处理每个基因树文件
for (file in gene_tree_files) {
  # 读取基因树
  gene_tree <- read.tree(file)
  
  # 确定外群名称为"DCYL"
  outgroup <- "DCYL"
  
  # 定义有根树
  rooted_tree <- root(gene_tree, outgroup = outgroup)
  
  # 构建输出文件路径
  output_file <- file.path(output_dir, basename(file))
  
  # 保存有根树
  write.tree(rooted_tree, file = output_file)
  
  # 打印处理信息
  cat("已将", file, "转化为有根树并保存至", output_file, "\n")
}

请确保在运行代码之前已经安装了`ape`包，并根据实际情况修改`input_dir`和`output_dir`变量的值。