diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml
deleted file mode 100644
index 74ec7b0..0000000
--- a/.github/workflows/rhub.yaml
+++ /dev/null
@@ -1,95 +0,0 @@
-# R-hub's generic GitHub Actions workflow file. It's canonical location is at
-# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
-# You can update this file to a newer version using the rhub2 package:
-#
-# rhub::rhub_setup()
-#
-# It is unlikely that you need to modify this file manually.
-
-name: R-hub
-run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
-
-on:
-  workflow_dispatch:
-    inputs:
-      config:
-        description: 'A comma separated list of R-hub platforms to use.'
-        type: string
-        default: 'linux,windows,macos'
-      name:
-        description: 'Run name. You can leave this empty now.'
-        type: string
-      id:
-        description: 'Unique ID. You can leave this empty now.'
-        type: string
-
-jobs:
-
-  setup:
-    runs-on: ubuntu-latest
-    outputs:
-      containers: ${{ steps.rhub-setup.outputs.containers }}
-      platforms: ${{ steps.rhub-setup.outputs.platforms }}
-
-    steps:
-    # NO NEED TO CHECKOUT HERE
-    - uses: r-hub/actions/setup@v1
-      with:
-        config: ${{ github.event.inputs.config }}
-      id: rhub-setup
-
-  linux-containers:
-    needs: setup
-    if: ${{ needs.setup.outputs.containers != '[]' }}
-    runs-on: ubuntu-latest
-    name: ${{ matrix.config.label }}
-    strategy:
-      fail-fast: false
-      matrix:
-        config: ${{ fromJson(needs.setup.outputs.containers) }}
-    container:
-      image: ${{ matrix.config.container }}
-
-    steps:
-      - uses: r-hub/actions/checkout@v1
-      - uses: r-hub/actions/platform-info@v1
-        with:
-          token: ${{ secrets.RHUB_TOKEN }}
-          job-config: ${{ matrix.config.job-config }}
-      - uses: r-hub/actions/setup-deps@v1
-        with:
-          token: ${{ secrets.RHUB_TOKEN }}
-          job-config: ${{ matrix.config.job-config }}
-      - uses: r-hub/actions/run-check@v1
-        with:
-          token: ${{ secrets.RHUB_TOKEN }}
-          job-config: ${{ matrix.config.job-config }}
-
-  other-platforms:
-    needs: setup
-    if: ${{ needs.setup.outputs.platforms != '[]' }}
-    runs-on: ${{ matrix.config.os }}
-    name: ${{ matrix.config.label }}
-    strategy:
-      fail-fast: false
-      matrix:
-        config: ${{ fromJson(needs.setup.outputs.platforms) }}
-
-    steps:
-      - uses: r-hub/actions/checkout@v1
-      - uses: r-hub/actions/setup-r@v1
-        with:
-          job-config: ${{ matrix.config.job-config }}
-          token: ${{ secrets.RHUB_TOKEN }}
-      - uses: r-hub/actions/platform-info@v1
-        with:
-          token: ${{ secrets.RHUB_TOKEN }}
-          job-config: ${{ matrix.config.job-config }}
-      - uses: r-hub/actions/setup-deps@v1
-        with:
-          job-config: ${{ matrix.config.job-config }}
-          token: ${{ secrets.RHUB_TOKEN }}
-      - uses: r-hub/actions/run-check@v1
-        with:
-          job-config: ${{ matrix.config.job-config }}
-          token: ${{ secrets.RHUB_TOKEN }}
diff --git a/.github/workflows/windows-check.yml b/.github/workflows/windows-check.yml
deleted file mode 100644
index e7643d8..0000000
--- a/.github/workflows/windows-check.yml
+++ /dev/null
@@ -1,63 +0,0 @@
-name: Windows Check
-
-on:
-  push:
-    branches: [ main ]
-  pull_request:
-    branches: [ main ]
-  workflow_dispatch:
-
-jobs:
-  windows-check:
-    runs-on: windows-latest
-    strategy:
-      matrix:
-        r-version: ['4.3', '4.4']
-
-    steps:
-    - uses: actions/checkout@v3
-
-    - name: Set up R ${{ matrix.r-version }}
-      uses: r-lib/actions/setup-r@v2
-      with:
-        r-version: ${{ matrix.r-version }}
-        
-    - name: Install Rtools
-      uses: r-lib/actions/setup-rtools@v2
-      if: runner.os == 'Windows'
-
-    - name: Query dependencies
-      run: |
-        install.packages('remotes')
-        saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-      shell: Rscript {0}
-
-    - name: Cache R packages
-      uses: actions/cache@v3
-      with:
-        path: ${{ env.R_LIBS_USER }}
-        key: ${{ runner.os }}-r-${{ matrix.r-version }}-${{ hashFiles('.github/depends.Rds') }}
-        restore-keys: ${{ runner.os }}-r-${{ matrix.r-version }}-
-
-    - name: Install dependencies
-      run: |
-        remotes::install_deps(dependencies = TRUE)
-      shell: Rscript {0}
-
-    - name: Check package
-      run: |
-        rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-      shell: Rscript {0}
-
-    - name: Test installation
-      run: |
-        install.packages(".", repos = NULL, type = "source")
-        library(MicrobiomeStat)
-      shell: Rscript {0}
-
-    - name: Upload check results
-      if: failure()
-      uses: actions/upload-artifact@v3
-      with:
-        name: ${{ runner.os }}-r${{ matrix.r-version }}-results
-        path: check
diff --git a/R/generate_taxa_cladogram_single.R b/R/generate_taxa_cladogram_single.R
index 24da34c..f4ef0cc 100644
--- a/R/generate_taxa_cladogram_single.R
+++ b/R/generate_taxa_cladogram_single.R
@@ -207,8 +207,23 @@ generate_taxa_cladogram_single <- function(
   fix_link_frame <- link_frame
   fix_link_frame[[min_label]] <- stringr::str_replace_all(fix_link_frame[[min_label]], pattern = " |\\(|\\)", replacement = "_")
   fix_link_frame[[min_label]] <- stringr::str_replace_all(fix_link_frame[[min_label]], pattern = "\\.", replacement = "")
-  # Build phylogenetic tree
-  treex <- build_tree(fix_link_frame, level_seq)
+  
+  # Check and use existing tree if available, otherwise build from taxonomy
+  if (!is.null(data.obj$tree)) {
+    tree <- data.obj$tree
+    # Ensure tree tips match our feature names
+    common_tips <- intersect(tree$tip.label, fix_link_frame[[min_label]])
+    if (length(common_tips) > 0) {
+      message("Using phylogenetic tree from data object.")
+      treex <- ape::keep.tip(tree, common_tips)
+    } else {
+      message("No matching tips found between phylogenetic tree and features. Using taxonomy-based tree instead.")
+      treex <- build_tree(fix_link_frame, level_seq)
+    }
+  } else {
+    message("Building taxonomy-based tree.")
+    treex <- build_tree(fix_link_frame, level_seq)
+  }
 
   # Join and process test results
   inputframe_linked <- join_frames(test.list, level_seq, link_frame)
diff --git a/tests/testthat/Rplots.pdf b/tests/testthat/Rplots.pdf
new file mode 100644
index 0000000..7fb70be
Binary files /dev/null and b/tests/testthat/Rplots.pdf differ
diff --git a/tests/testthat/test-generate_taxa_cladogram_single.R b/tests/testthat/test-generate_taxa_cladogram_single.R
new file mode 100644
index 0000000..7e087b5
--- /dev/null
+++ b/tests/testthat/test-generate_taxa_cladogram_single.R
@@ -0,0 +1,123 @@
+test_that("generate_taxa_cladogram_single works with and without phylogenetic tree", {
+  # Create mock data objects with more realistic taxonomic structure
+  features <- paste0("ASV", 1:5)  # 使用简单的ASV标识符
+
+  # Create feature annotation data frame - 避免使用可能冲突的列名
+  feature.ann <- data.frame(
+    tax_Kingdom = rep("Bacteria", 5),
+    tax_Phylum = c("Firmicutes", "Firmicutes", "Bacteroidetes", "Bacteroidetes", "Proteobacteria"),
+    tax_Class = c("Bacilli", "Clostridia", "Bacteroidia", "Flavobacteriia", "Gammaproteobacteria"),
+    row.names = features,
+    stringsAsFactors = FALSE
+  )
+
+  # Create abundance matrix
+  feature.tab <- matrix(
+    rpois(50, lambda = 10),
+    nrow = 5,
+    ncol = 10,
+    dimnames = list(features, paste0("Sample", 1:10))
+  )
+
+  # Create metadata
+  meta.dat <- data.frame(
+    Group = rep(c("A", "B"), each = 5),
+    row.names = paste0("Sample", 1:10)
+  )
+
+  # Create base data object
+  data.obj.no.tree <- list(
+    feature.tab = feature.tab,
+    feature.ann = feature.ann,
+    meta.dat = meta.dat
+  )
+
+  # Create mock test results
+  test.list <- list(
+    tax_Phylum = list(
+      "A_vs_B" = data.frame(
+        Feature = unique(feature.ann$tax_Phylum),
+        Coefficient = rnorm(3),
+        P.Value = runif(3),
+        Adjusted.P.Value = runif(3)
+      )
+    ),
+    tax_Class = list(
+      "A_vs_B" = data.frame(
+        Feature = unique(feature.ann$tax_Class),
+        Coefficient = rnorm(5),
+        P.Value = runif(5),
+        Adjusted.P.Value = runif(5)
+      )
+    )
+  )
+
+  # Create data object with tree - 确保树的标签与特征完全匹配
+  library(ape)
+  tree <- ape::read.tree(text = paste0("(", paste(features, collapse = ","), ");"))
+  tree$edge.length <- rep(1, nrow(tree$edge))
+  # 添加必要的属性
+  tree$node.label <- paste0("Node", 1:(tree$Nnode))
+
+  data.obj.with.tree <- data.obj.no.tree
+  data.obj.with.tree$tree <- tree
+
+  # Test cases
+  suppressWarnings({
+    # Test case 1: Without tree
+    result_no_tree <- capture_messages({
+      plot.list.no.tree <- generate_taxa_cladogram_single(
+        data.obj = data.obj.no.tree,
+        test.list = test.list,
+        group.var = "Group",
+        feature.level = c("tax_Phylum", "tax_Class"),
+        color.group.level = "tax_Phylum"
+      )
+    })
+    expect_true(any(grepl("Building taxonomy-based tree", result_no_tree)))
+
+    # Test case 2: With tree
+    result_with_tree <- capture_messages({
+      plot.list.with.tree <- generate_taxa_cladogram_single(
+        data.obj = data.obj.with.tree,
+        test.list = test.list,
+        group.var = "Group",
+        feature.level = c("tax_Phylum", "tax_Class"),
+        color.group.level = "tax_Phylum"
+      )
+    })
+    cat("\nActual messages with tree:\n")
+    print(result_with_tree)
+
+    # Test case 3: With mismatched tree
+    mismatched_tree <- ape::read.tree(text = "(Wrong1,Wrong2,Wrong3,Wrong4,Wrong5);")
+    mismatched_tree$edge.length <- rep(1, nrow(mismatched_tree$edge))
+    data.obj.mismatched <- data.obj.no.tree
+    data.obj.mismatched$tree <- mismatched_tree
+
+    result_mismatched <- capture_messages({
+      plot.list.mismatched <- generate_taxa_cladogram_single(
+        data.obj = data.obj.mismatched,
+        test.list = test.list,
+        group.var = "Group",
+        feature.level = c("tax_Phylum", "tax_Class"),
+        color.group.level = "tax_Phylum"
+      )
+    })
+  })
+
+  # Basic checks
+  expect_type(plot.list.no.tree, "list")
+  expect_type(plot.list.with.tree, "list")
+  expect_type(plot.list.mismatched, "list")
+
+  # Check list contents
+  expect_true(all(sapply(plot.list.no.tree, function(x) inherits(x, "ggplot"))))
+  expect_true(all(sapply(plot.list.with.tree, function(x) inherits(x, "ggplot"))))
+  expect_true(all(sapply(plot.list.mismatched, function(x) inherits(x, "ggplot"))))
+
+  # Check list length
+  expect_length(plot.list.no.tree, 1)
+  expect_length(plot.list.with.tree, 1)
+  expect_length(plot.list.mismatched, 1)
+})