diff --git a/environment.yml b/environment.yml
index 847e7d4..d12ebde 100644
--- a/environment.yml
+++ b/environment.yml
@@ -4,8 +4,8 @@ channels:
     - bioconda
     - defaults
 dependencies:
-    - sourmash>=4.8.8,<5
-    - sourmash_plugin_branchwater>=0.9.7
+    - sourmash>=4.9.2,<5
+    - sourmash_plugin_branchwater>=0.9.13,<1
     - pip
     - pytest
     - matplotlib
@@ -17,6 +17,6 @@ dependencies:
     - seaborn
     - plotly
     - biopython
-    - ete3>=3.1.3,<4
+    - ete4>=4.3.0,<5
     - pip:
       - kaleido
diff --git a/pyproject.toml b/pyproject.toml
index 2ad1b83..67f941e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,7 @@ version = "0.5.1"
 dependencies = ["sourmash>=4.9.2,<5", "sourmash_utils>=0.2",
                 "matplotlib", "numpy", "scipy", "scikit-learn",
                 "seaborn", "upsetplot", "matplotlib_venn", "pandas",
-                "plotly", "biopython", "ete3", "kaleido", "pyqt5",
+                "plotly", "biopython", "ete4", "kaleido", "pyqt6",
                 "legacy_cgi"]
 
 [build-system]