diff --git a/src/hmmer3/hmmer3/.gitignore b/src/hmmer3/.gitignore
similarity index 100%
rename from src/hmmer3/hmmer3/.gitignore
rename to src/hmmer3/.gitignore
diff --git a/src/hmmer3/Makefile b/src/hmmer3/Makefile
old mode 100755
new mode 100644
index 165f386..977c199
--- a/src/hmmer3/Makefile
+++ b/src/hmmer3/Makefile
@@ -2,12 +2,10 @@
 # $Id: $
 # ---------------------------------------------------------------
 # @file: Makefile
-# @desc: makefile for lxpack
+# @desc: makefile for package exonerate
 #
 # @history:
-# @history:
-# @+	    <Gloup> : Apr 97 : Created
-# @+	    <Gloup> : Mar 02 : Updated for LXxware
+# @+	    <Gloup> : Sept 15 : Adapted to ORG.Annot
 #
 # @note: should be processed with gnu compatible make
 # @note: helixware_compatible
@@ -15,14 +13,16 @@
 # @end:
 # ---------------------------------------------------------------
 #
+
 include ../../config/auto.conf
 
-DIRS = hmmer3
+PKG = hmmer-3.1b1
 
-include ../../config/targets/propagate.targ
+include $(CFGDIR)targets/package.targ
 
-include ../../config/targets/help.targ
+include $(CFGDIR)targets/help.targ
 
+# bug fix
 all::
-	$(MAKE) ACTION=$@ _action
+	-mkdir $(PKGDIR)/userguide
 
diff --git a/src/hmmer3/hmmer-3.1b1.tgz b/src/hmmer3/hmmer-3.1b1.tgz
new file mode 100644
index 0000000..c7e3a3f
Binary files /dev/null and b/src/hmmer3/hmmer-3.1b1.tgz differ
diff --git a/src/hmmer3/hmmer3/Makefile b/src/hmmer3/hmmer3/Makefile
deleted file mode 100644
index dcccf17..0000000
--- a/src/hmmer3/hmmer3/Makefile
+++ /dev/null
@@ -1,24 +0,0 @@
-# ---------------------------------------------------------------
-# $Id: $
-# ---------------------------------------------------------------
-# @file: Makefile
-# @desc: makefile for package exonerate
-#
-# @history:
-# @+	    <Gloup> : Sept 15 : Adapted to ORG.Annot
-#
-# @note: should be processed with gnu compatible make
-# @note: helixware_compatible
-#
-# @end:
-# ---------------------------------------------------------------
-#
-
-include ../../../config/auto.conf
-
-PKG = hmmer-3.1b1
-
-include $(CFGDIR)targets/package.targ
-
-include $(CFGDIR)targets/help.targ
-
diff --git a/src/hmmer3/hmmer3/hmmer-3.1b1.tgz b/src/hmmer3/hmmer3/hmmer-3.1b1.tgz
deleted file mode 100644
index e850af4..0000000
Binary files a/src/hmmer3/hmmer3/hmmer-3.1b1.tgz and /dev/null differ