diff --git a/req_m2m_gha.txt b/req_m2m_gha.txt
index ef43998..fa0f3f8 100644
--- a/req_m2m_gha.txt
+++ b/req_m2m_gha.txt
@@ -2,8 +2,8 @@ biopython==1.74
 clyngor>=0.3.31
 clyngor-with-clingo>=5.3.post1
 ete3==3.1.1
-MeneTools>=2.0.6
-Miscoto>=2.0.7
+MeneTools>=3.0.2
+Miscoto>=3.0.2
 mpwt>=0.5.4
 padmet>=4.0
 powergrasp==0.8.18
diff --git a/requirements.txt b/requirements.txt
index ab68e1f..393e0c8 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -21,9 +21,9 @@ importlib-metadata==1.6.0
 kiwisolver==1.2.0
 lxml==4.3.4
 matplotlib==3.1.1
-MeneTools==2.0.6
+MeneTools==3.0.2
 Metage2Metabo==1.1.6
-Miscoto==2.1.2
+Miscoto==3.0.2
 more-itertools==8.2.0
 mpmath==1.1.0
 mpwt==0.5.4
diff --git a/requirements_m2m_analysis.txt b/requirements_m2m_analysis.txt
index 0b3cf76..7fff615 100644
--- a/requirements_m2m_analysis.txt
+++ b/requirements_m2m_analysis.txt
@@ -15,8 +15,8 @@ future==0.17.1
 gffutils==0.9
 graphviz==0.13
 importlib-metadata==0.17
-MeneTools>=2.0.3
-Miscoto>=2.1.1
+MeneTools>=3.0.2
+Miscoto>=3.0.2
 more-itertools==7.0.0
 mpmath==1.1.0
 mpwt>=0.5.3