diff --git a/tools/patser/.shed.yml.deprecated b/deprecated/patser/.shed.yml.deprecated
similarity index 100%
rename from tools/patser/.shed.yml.deprecated
rename to deprecated/patser/.shed.yml.deprecated
diff --git a/tools/patser/patser-v3e.xml b/deprecated/patser/patser-v3e.xml
similarity index 100%
rename from tools/patser/patser-v3e.xml
rename to deprecated/patser/patser-v3e.xml
diff --git a/tools/patser/test-data/EcR_USP_224.fa b/deprecated/patser/test-data/EcR_USP_224.fa
similarity index 100%
rename from tools/patser/test-data/EcR_USP_224.fa
rename to deprecated/patser/test-data/EcR_USP_224.fa
diff --git a/tools/patser/test-data/PWM_training_EcR-USP.txt b/deprecated/patser/test-data/PWM_training_EcR-USP.txt
similarity index 100%
rename from tools/patser/test-data/PWM_training_EcR-USP.txt
rename to deprecated/patser/test-data/PWM_training_EcR-USP.txt
diff --git a/tools/patser/test-data/output.txt b/deprecated/patser/test-data/output.txt
similarity index 100%
rename from tools/patser/test-data/output.txt
rename to deprecated/patser/test-data/output.txt
diff --git a/tools/patser/tool_dependencies.xml b/deprecated/patser/tool_dependencies.xml
similarity index 100%
rename from tools/patser/tool_dependencies.xml
rename to deprecated/patser/tool_dependencies.xml