library(ape) species_tree <- read.tree("species_tree.treefile") gene_tree <- read.tree("gene1.treefile") comparePhylo(tree.nwk,species_tree,force.rooted = TRUE)请你根据上述代码。帮我写一段用R的ape包，批量对比1个物种树和多个基因树拓扑结构差异的代码。统计有多少基因树与物种树不一致。

当然，我可以帮你完成这个任务。以下是使用R的ape包批量比较一个物种树和多个基因树拓扑结构差异的代码：

library(ape)
species_tree <- read.tree("species_tree.treefile")

# 定义一个函数来比较树拓扑结构差异
compare_trees <- function(gene_tree_file, species_tree) {
  gene_tree <- read.tree(gene_tree_file)
  diff_count <- comparePhylo(gene_tree, species_tree, force.rooted = TRUE)
  return(diff_count)
}

# 定义一个函数来批量比较基因树和物种树的差异
batch_compare_trees <- function(gene_tree_files, species_tree) {
  diff_counts <- numeric(length(gene_tree_files))
  for (i in seq_along(gene_tree_files)) {
    gene_tree_file <- gene_tree_files[i]
    diff_counts[i] <- compare_trees(gene_tree_file, species_tree)
  }
  return(diff_counts)
}

# 设置基因树文件路径
gene_tree_files <- c("gene1.treefile", "gene2.treefile", "gene3.treefile") # 将文件名替换为你的基因树文件

# 执行批量比较
diff_counts <- batch_compare_trees(gene_tree_files, species_tree)

# 统计不一致的基因树数量
inconsistent_count <- sum(diff_counts != 0)
print(paste("有", inconsistent_count, "个基因树与物种树不一致。"))

请确保将`gene1.treefile`替换为你的基因树文件的路径，并根据需要更新`gene_tree_files`向量来包含所有基因树文件的路径。执行这段代码后，你将得到一个输出，显示有多少个基因树与物种树的拓扑结构不一致。