diff --git a/repeatexplorer2/.shed.yml b/tools/repeatexplorer2/.shed.yml
similarity index 100%
rename from repeatexplorer2/.shed.yml
rename to tools/repeatexplorer2/.shed.yml
diff --git a/repeatexplorer2/repex_full_clustering.xml b/tools/repeatexplorer2/repex_full_clustering.xml
similarity index 100%
rename from repeatexplorer2/repex_full_clustering.xml
rename to tools/repeatexplorer2/repex_full_clustering.xml
diff --git a/repeatexplorer2/repex_tarean.xml b/tools/repeatexplorer2/repex_tarean.xml
similarity index 100%
rename from repeatexplorer2/repex_tarean.xml
rename to tools/repeatexplorer2/repex_tarean.xml