diff --git a/lib/galaxy/tools/util/__init__.py b/lib/galaxy/tools/util/__init__.py
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/tools/hyphy/hyphy_util.py b/lib/galaxy/tools/util/hyphy_util.py
similarity index 100%
rename from tools/hyphy/hyphy_util.py
rename to lib/galaxy/tools/util/hyphy_util.py
diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 619465d7ea9..0223fef7eab 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -127,9 +127,9 @@
 	-->
   </section>
  <section name="Evolution: HyPhy" id="hyphy">
-    <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />
-    <tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
-    <tool file="hyphy/hyphy_dnds_wrapper.xml" />
+    <tool file="hyphy/hyphy_branch_lengths_wrapper1/1.0.0/hyphy_branch_lengths_wrapper.xml" />
+    <tool file="hyphy/hyphy_nj_tree_wrapper1/1.0.0/hyphy_nj_tree_wrapper.xml" />
+    <tool file="hyphy/hyphy_dnds_wrapper1/1.0.0/hyphy_dnds_wrapper.xml" />
  </section>
  <!--
  These are deprecated
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index f4ac190525c..7b43b5d1770 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -130,9 +130,9 @@
 	<tool file="regVariation/getIndels_3way.xml" />
   </section>
  <section name="Evolution: HyPhy" id="hyphy">
-    <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />
-    <tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
-    <tool file="hyphy/hyphy_dnds_wrapper.xml" />
+    <tool file="hyphy/hyphy_branch_lengths_wrapper1/1.0.0/hyphy_branch_lengths_wrapper.xml" />
+    <tool file="hyphy/hyphy_nj_tree_wrapper1/1.0.0/hyphy_nj_tree_wrapper.xml" />
+    <tool file="hyphy/hyphy_dnds_wrapper1/1.0.0/hyphy_dnds_wrapper.xml" />
  </section>
  <!--
  These are deprecated
diff --git a/tools/hyphy/hyphy_branch_lengths_wrapper.py b/tools/hyphy/hyphy_branch_lengths_wrapper1/1.0.0/hyphy_branch_lengths_wrapper.py
similarity index 95%
rename from tools/hyphy/hyphy_branch_lengths_wrapper.py
rename to tools/hyphy/hyphy_branch_lengths_wrapper1/1.0.0/hyphy_branch_lengths_wrapper.py
index dd17ec8257e..3345e7100c1 100644
--- a/tools/hyphy/hyphy_branch_lengths_wrapper.py
+++ b/tools/hyphy/hyphy_branch_lengths_wrapper1/1.0.0/hyphy_branch_lengths_wrapper.py
@@ -1,7 +1,7 @@
 #Dan Blankenberg
 #takes commandline tree def and input multiple fasta alignment file and runs the branch length ananlysis
 import os, sys
-import hyphy_util
+from galaxy.tools.util import hyphy_util
 
 #Retrieve hard coded hyphy path, this will need to be the same across the cluster
 HYPHY_PATH = hyphy_util.HYPHY_PATH
diff --git a/tools/hyphy/hyphy_branch_lengths_wrapper.xml b/tools/hyphy/hyphy_branch_lengths_wrapper1/1.0.0/hyphy_branch_lengths_wrapper.xml
similarity index 100%
rename from tools/hyphy/hyphy_branch_lengths_wrapper.xml
rename to tools/hyphy/hyphy_branch_lengths_wrapper1/1.0.0/hyphy_branch_lengths_wrapper.xml
diff --git a/tools/hyphy/hyphy_dnds_wrapper.py b/tools/hyphy/hyphy_dnds_wrapper1/1.0.0/hyphy_dnds_wrapper.py
similarity index 95%
rename from tools/hyphy/hyphy_dnds_wrapper.py
rename to tools/hyphy/hyphy_dnds_wrapper1/1.0.0/hyphy_dnds_wrapper.py
index 057e9c5c38b..18e3d958062 100644
--- a/tools/hyphy/hyphy_dnds_wrapper.py
+++ b/tools/hyphy/hyphy_dnds_wrapper1/1.0.0/hyphy_dnds_wrapper.py
@@ -1,7 +1,7 @@
 #Guru
 #takes fasta alignments, a distance metric and builds neighbor joining trees
 import os, sys
-import hyphy_util
+from galaxy.tools.util import hyphy_util
 
 #Retrieve hard coded hyphy path, this will need to be the same across the cluster
 HYPHY_PATH = hyphy_util.HYPHY_PATH
diff --git a/tools/hyphy/hyphy_dnds_wrapper.xml b/tools/hyphy/hyphy_dnds_wrapper1/1.0.0/hyphy_dnds_wrapper.xml
similarity index 100%
rename from tools/hyphy/hyphy_dnds_wrapper.xml
rename to tools/hyphy/hyphy_dnds_wrapper1/1.0.0/hyphy_dnds_wrapper.xml
diff --git a/tools/hyphy/hyphy_nj_tree_wrapper.py b/tools/hyphy/hyphy_nj_tree_wrapper1/1.0.0/hyphy_nj_tree_wrapper.py
similarity index 95%
rename from tools/hyphy/hyphy_nj_tree_wrapper.py
rename to tools/hyphy/hyphy_nj_tree_wrapper1/1.0.0/hyphy_nj_tree_wrapper.py
index edc519239ea..719793c9c91 100644
--- a/tools/hyphy/hyphy_nj_tree_wrapper.py
+++ b/tools/hyphy/hyphy_nj_tree_wrapper1/1.0.0/hyphy_nj_tree_wrapper.py
@@ -1,7 +1,7 @@
 #Dan Blankenberg
 #takes fasta alignments, a distance metric and builds neighbor joining trees
 import os, sys
-import hyphy_util
+from galaxy.tools.util import hyphy_util
 
 #Retrieve hard coded hyphy path, this will need to be the same across the cluster
 HYPHY_PATH = hyphy_util.HYPHY_PATH
diff --git a/tools/hyphy/hyphy_nj_tree_wrapper.xml b/tools/hyphy/hyphy_nj_tree_wrapper1/1.0.0/hyphy_nj_tree_wrapper.xml
similarity index 100%
rename from tools/hyphy/hyphy_nj_tree_wrapper.xml
rename to tools/hyphy/hyphy_nj_tree_wrapper1/1.0.0/hyphy_nj_tree_wrapper.xml