diff --git a/.github/workflows/add_source_to_release.yml b/.github/workflows/add_source_to_release.yml
index f5a025f..f843a24 100644
--- a/.github/workflows/add_source_to_release.yml
+++ b/.github/workflows/add_source_to_release.yml
@@ -17,7 +17,7 @@ jobs:
 
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
           submodules: recursive
diff --git a/.github/workflows/build_container.yml b/.github/workflows/build_container.yml
index 2165283..93a506a 100644
--- a/.github/workflows/build_container.yml
+++ b/.github/workflows/build_container.yml
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Login to GitHub Container Registry
         run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u iqtree --password-stdin
diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
index 0162e34..aa177b4 100644
--- a/.github/workflows/build_docs.yml
+++ b/.github/workflows/build_docs.yml
@@ -22,7 +22,7 @@ jobs:
     name: Fetch or Build IQ-TREE Static Library
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
           submodules: recursive
@@ -40,7 +40,7 @@ jobs:
     needs: build-iqtree
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
           submodules: recursive
diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index b7c27a7..3f9d25f 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -30,7 +30,7 @@ jobs:
           platform_id: win_amd64
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
           submodules: recursive
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 94d6b05..b031ef0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -24,7 +24,7 @@ jobs:
         os: [ubuntu-latest, macos-15-intel, macos-15, windows-latest] # Intel linux, Intel Mac, ARM Mac, Windows
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
           submodules: recursive
@@ -46,7 +46,7 @@ jobs:
         os: [ubuntu-latest, macos-15-intel, macos-15, windows-latest] # Intel linux, Intel Mac, ARM Mac, Windows
         python-version: ["3.11", "3.12", "3.13"]
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
           submodules: recursive
@@ -102,7 +102,7 @@ jobs:
         os: [ubuntu-latest]
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -127,7 +127,7 @@ jobs:
         os: [ubuntu-latest]
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -152,7 +152,7 @@ jobs:
         os: [ubuntu-latest]
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
           submodules: recursive
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index ee388ce..b1d7ce1 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -30,7 +30,7 @@ jobs:
           platform_id: win_amd64
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
           submodules: recursive
@@ -87,7 +87,7 @@ jobs:
     name: Fetch or Build IQ-TREE Static Library
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
           submodules: recursive
@@ -105,7 +105,7 @@ jobs:
     needs: build-iqtree
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
           submodules: recursive