diff --git a/config/default.conf b/config/default.conf
index 8bdb54c..566a765 100644
--- a/config/default.conf
+++ b/config/default.conf
@@ -118,10 +118,12 @@ INCDIR	 =	$(abspath $(PRTDIR))/include
 # default gmake variable in implicit rules
 # ------------------------------------
 
-CFLAGS 	  := $(CFLAGS)	$(OPTIM) $(MACHDEF) -I$(INCDIR)
+#CFLAGS 	  := $(CFLAGS) $(OPTIM) $(MACHDEF) -I$(INCDIR)
+CFLAGS 	  = $(OPTIM) $(MACHDEF) -I$(INCDIR)
 
-LDFLAGS	  := $(LDFLAGS)    -L$(LIBDIR) -L.
+#LDFLAGS	  := $(LDFLAGS) -L$(LIBDIR) -L.
+LDFLAGS	  = -L$(LIBDIR) -L.
 
-LDLIBS	  =	    $(LIBS) $(MALLOC_LIBS) $(MATH_LIBS) $(CC_LIBS)
+LDLIBS	  =	$(LIBS) $(MALLOC_LIBS) $(MATH_LIBS) $(CC_LIBS)
 
-LINTFLAGS = 	$(MACHDEF) -I$(INCDIR)
+LINTFLAGS = $(MACHDEF) -I$(INCDIR)
diff --git a/config/targets/lxbin.targ b/config/targets/lxbin.targ
index 4e6dbe9..f8063f5 100644
--- a/config/targets/lxbin.targ
+++ b/config/targets/lxbin.targ
@@ -34,7 +34,7 @@ all::	prelib $(PROGS) install
 
 prelib::
 	test -d $(PRTDIR) || mkdir $(PRTDIR)  # because some linker may complain
-	test -d $(LIBDIR) || mkdir $(LIBDIR)  # if -L$(LIBDIR) does not exist
+	test -d $(LIBDIR) || mkdir $(LIBDIR)  # if LIBDIR does not exist
 
 install::
 	test -d $(PRTDIR) || mkdir $(PRTDIR)
diff --git a/config/targets/package.targ b/config/targets/package.targ
index 40550dc..55733de 100644
--- a/config/targets/package.targ
+++ b/config/targets/package.targ
@@ -31,7 +31,6 @@ pkg.expand::
 	test -f $(PKGDIR)/configure || $(TAR) zxf $(PKGTAR) -C $(PKGDIR) --strip-components 1
 
 pkg.make:: pkg.expand
-	echo $(PKG_CONFIG)
 	test -f $(PKGDIR)/Makefile || (export PATH="$(PRTPATH_BIN):$$PATH" && \
 	                               export PKG_CONFIG=$(PKG_CONFIG) && \
 	                               export CC="$(CC)" && \
diff --git a/src/hmmer3/Makefile b/src/hmmer3/Makefile
index 977c199..b101e2f 100644
--- a/src/hmmer3/Makefile
+++ b/src/hmmer3/Makefile
@@ -22,7 +22,3 @@ include $(CFGDIR)targets/package.targ
 
 include $(CFGDIR)targets/help.targ
 
-# bug fix
-all::
-	-mkdir $(PKGDIR)/userguide
-
diff --git a/src/kimono/Makefile b/src/kimono/Makefile
index c9e9752..7aec888 100755
--- a/src/kimono/Makefile
+++ b/src/kimono/Makefile
@@ -22,9 +22,3 @@ DIRS = lxpack
 include ../../config/targets/propagate.targ
 
 include ../../config/targets/help.targ
-
-all::
-	$(MAKE) ACTION=$@ _action
-
-clean::
-	$(MAKE) -C lxpack portclean
diff --git a/src/muscle/Makefile b/src/muscle/Makefile
index 6e300a0..d0fb99f 100755
--- a/src/muscle/Makefile
+++ b/src/muscle/Makefile
@@ -22,9 +22,3 @@ DIRS = muscle3.8.31
 include ../../config/targets/propagate.targ
 
 include ../../config/targets/help.targ
-
-all::
-	$(MAKE) ACTION=$@ _action
-
-clean::
-	$(MAKE) -C lxpack portclean
diff --git a/src/muscle/muscle3.8.31/Makefile b/src/muscle/muscle3.8.31/Makefile
index d16c191..c9841e9 100755
--- a/src/muscle/muscle3.8.31/Makefile
+++ b/src/muscle/muscle3.8.31/Makefile
@@ -2,29 +2,24 @@
 # $Id: $
 # ---------------------------------------------------------------
 # @file: Makefile
-# @desc: makefile for lxpack
-#
-# @history:
-# @history:
-# @+	    <Gloup> : Apr 97 : Created
-# @+	    <Gloup> : Mar 02 : Updated for LXxware
-#
-# @note: should be processed with gnu compatible make
-# @note: helixware_compatible
-#
-# @end:
+# @desc: makefile for muscle
 # ---------------------------------------------------------------
 #
 include ../../../config/auto.conf
 
-DIRS = src
+all: muscle install 
 
-include ../../../config/targets/propagate.targ
+muscle:
+	chmod +x ./mk
+	(export CXX=$(CXX) && ./mk)
 
-include ../../../config/targets/help.targ
+test:
 
-all::
-	$(MAKE) ACTION=$@ _action
+install:
+	cp muscle $(BINDIR)
+	
+clean:
+	-\rm -f *.o muscle
 
-clean::
-	$(MAKE) -C lxpack portclean
+portclean: clean
+	-\rm -f $(BINDIR)/muscle
diff --git a/src/muscle/muscle3.8.31/src/README.txt b/src/muscle/muscle3.8.31/README.txt
similarity index 100%
rename from src/muscle/muscle3.8.31/src/README.txt
rename to src/muscle/muscle3.8.31/README.txt
diff --git a/src/muscle/muscle3.8.31/src/aligngivenpath.cpp b/src/muscle/muscle3.8.31/aligngivenpath.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/aligngivenpath.cpp
rename to src/muscle/muscle3.8.31/aligngivenpath.cpp
diff --git a/src/muscle/muscle3.8.31/src/aligngivenpathsw.cpp b/src/muscle/muscle3.8.31/aligngivenpathsw.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/aligngivenpathsw.cpp
rename to src/muscle/muscle3.8.31/aligngivenpathsw.cpp
diff --git a/src/muscle/muscle3.8.31/src/aligntwomsas.cpp b/src/muscle/muscle3.8.31/aligntwomsas.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/aligntwomsas.cpp
rename to src/muscle/muscle3.8.31/aligntwomsas.cpp
diff --git a/src/muscle/muscle3.8.31/src/aligntwoprofs.cpp b/src/muscle/muscle3.8.31/aligntwoprofs.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/aligntwoprofs.cpp
rename to src/muscle/muscle3.8.31/aligntwoprofs.cpp
diff --git a/src/muscle/muscle3.8.31/src/aln.cpp b/src/muscle/muscle3.8.31/aln.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/aln.cpp
rename to src/muscle/muscle3.8.31/aln.cpp
diff --git a/src/muscle/muscle3.8.31/src/alpha.cpp b/src/muscle/muscle3.8.31/alpha.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/alpha.cpp
rename to src/muscle/muscle3.8.31/alpha.cpp
diff --git a/src/muscle/muscle3.8.31/src/alpha.h b/src/muscle/muscle3.8.31/alpha.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/alpha.h
rename to src/muscle/muscle3.8.31/alpha.h
diff --git a/src/muscle/muscle3.8.31/src/anchors.cpp b/src/muscle/muscle3.8.31/anchors.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/anchors.cpp
rename to src/muscle/muscle3.8.31/anchors.cpp
diff --git a/src/muscle/muscle3.8.31/src/bittraceback.cpp b/src/muscle/muscle3.8.31/bittraceback.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/bittraceback.cpp
rename to src/muscle/muscle3.8.31/bittraceback.cpp
diff --git a/src/muscle/muscle3.8.31/src/blosum62.cpp b/src/muscle/muscle3.8.31/blosum62.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/blosum62.cpp
rename to src/muscle/muscle3.8.31/blosum62.cpp
diff --git a/src/muscle/muscle3.8.31/src/blosumla.cpp b/src/muscle/muscle3.8.31/blosumla.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/blosumla.cpp
rename to src/muscle/muscle3.8.31/blosumla.cpp
diff --git a/src/muscle/muscle3.8.31/src/clust.cpp b/src/muscle/muscle3.8.31/clust.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/clust.cpp
rename to src/muscle/muscle3.8.31/clust.cpp
diff --git a/src/muscle/muscle3.8.31/src/clust.h b/src/muscle/muscle3.8.31/clust.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/clust.h
rename to src/muscle/muscle3.8.31/clust.h
diff --git a/src/muscle/muscle3.8.31/src/cluster.cpp b/src/muscle/muscle3.8.31/cluster.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/cluster.cpp
rename to src/muscle/muscle3.8.31/cluster.cpp
diff --git a/src/muscle/muscle3.8.31/src/cluster.h b/src/muscle/muscle3.8.31/cluster.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/cluster.h
rename to src/muscle/muscle3.8.31/cluster.h
diff --git a/src/muscle/muscle3.8.31/src/clustset.h b/src/muscle/muscle3.8.31/clustset.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/clustset.h
rename to src/muscle/muscle3.8.31/clustset.h
diff --git a/src/muscle/muscle3.8.31/src/clustsetdf.h b/src/muscle/muscle3.8.31/clustsetdf.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/clustsetdf.h
rename to src/muscle/muscle3.8.31/clustsetdf.h
diff --git a/src/muscle/muscle3.8.31/src/clustsetmsa.h b/src/muscle/muscle3.8.31/clustsetmsa.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/clustsetmsa.h
rename to src/muscle/muscle3.8.31/clustsetmsa.h
diff --git a/src/muscle/muscle3.8.31/src/clwwt.cpp b/src/muscle/muscle3.8.31/clwwt.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/clwwt.cpp
rename to src/muscle/muscle3.8.31/clwwt.cpp
diff --git a/src/muscle/muscle3.8.31/src/color.cpp b/src/muscle/muscle3.8.31/color.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/color.cpp
rename to src/muscle/muscle3.8.31/color.cpp
diff --git a/src/muscle/muscle3.8.31/src/cons.cpp b/src/muscle/muscle3.8.31/cons.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/cons.cpp
rename to src/muscle/muscle3.8.31/cons.cpp
diff --git a/src/muscle/muscle3.8.31/src/diaglist.cpp b/src/muscle/muscle3.8.31/diaglist.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/diaglist.cpp
rename to src/muscle/muscle3.8.31/diaglist.cpp
diff --git a/src/muscle/muscle3.8.31/src/diaglist.h b/src/muscle/muscle3.8.31/diaglist.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/diaglist.h
rename to src/muscle/muscle3.8.31/diaglist.h
diff --git a/src/muscle/muscle3.8.31/src/diffobjscore.cpp b/src/muscle/muscle3.8.31/diffobjscore.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/diffobjscore.cpp
rename to src/muscle/muscle3.8.31/diffobjscore.cpp
diff --git a/src/muscle/muscle3.8.31/src/diffpaths.cpp b/src/muscle/muscle3.8.31/diffpaths.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/diffpaths.cpp
rename to src/muscle/muscle3.8.31/diffpaths.cpp
diff --git a/src/muscle/muscle3.8.31/src/difftrees.cpp b/src/muscle/muscle3.8.31/difftrees.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/difftrees.cpp
rename to src/muscle/muscle3.8.31/difftrees.cpp
diff --git a/src/muscle/muscle3.8.31/src/difftreese.cpp b/src/muscle/muscle3.8.31/difftreese.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/difftreese.cpp
rename to src/muscle/muscle3.8.31/difftreese.cpp
diff --git a/src/muscle/muscle3.8.31/src/distcalc.cpp b/src/muscle/muscle3.8.31/distcalc.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/distcalc.cpp
rename to src/muscle/muscle3.8.31/distcalc.cpp
diff --git a/src/muscle/muscle3.8.31/src/distcalc.h b/src/muscle/muscle3.8.31/distcalc.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/distcalc.h
rename to src/muscle/muscle3.8.31/distcalc.h
diff --git a/src/muscle/muscle3.8.31/src/distfunc.cpp b/src/muscle/muscle3.8.31/distfunc.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/distfunc.cpp
rename to src/muscle/muscle3.8.31/distfunc.cpp
diff --git a/src/muscle/muscle3.8.31/src/distfunc.h b/src/muscle/muscle3.8.31/distfunc.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/distfunc.h
rename to src/muscle/muscle3.8.31/distfunc.h
diff --git a/src/muscle/muscle3.8.31/src/distpwkimura.cpp b/src/muscle/muscle3.8.31/distpwkimura.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/distpwkimura.cpp
rename to src/muscle/muscle3.8.31/distpwkimura.cpp
diff --git a/src/muscle/muscle3.8.31/src/domuscle.cpp b/src/muscle/muscle3.8.31/domuscle.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/domuscle.cpp
rename to src/muscle/muscle3.8.31/domuscle.cpp
diff --git a/src/muscle/muscle3.8.31/src/dosp.cpp b/src/muscle/muscle3.8.31/dosp.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/dosp.cpp
rename to src/muscle/muscle3.8.31/dosp.cpp
diff --git a/src/muscle/muscle3.8.31/src/dpregionlist.h b/src/muscle/muscle3.8.31/dpregionlist.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/dpregionlist.h
rename to src/muscle/muscle3.8.31/dpregionlist.h
diff --git a/src/muscle/muscle3.8.31/src/dpreglist.cpp b/src/muscle/muscle3.8.31/dpreglist.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/dpreglist.cpp
rename to src/muscle/muscle3.8.31/dpreglist.cpp
diff --git a/src/muscle/muscle3.8.31/src/dpreglist.h b/src/muscle/muscle3.8.31/dpreglist.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/dpreglist.h
rename to src/muscle/muscle3.8.31/dpreglist.h
diff --git a/src/muscle/muscle3.8.31/src/drawtree.cpp b/src/muscle/muscle3.8.31/drawtree.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/drawtree.cpp
rename to src/muscle/muscle3.8.31/drawtree.cpp
diff --git a/src/muscle/muscle3.8.31/src/edgelist.cpp b/src/muscle/muscle3.8.31/edgelist.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/edgelist.cpp
rename to src/muscle/muscle3.8.31/edgelist.cpp
diff --git a/src/muscle/muscle3.8.31/src/edgelist.h b/src/muscle/muscle3.8.31/edgelist.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/edgelist.h
rename to src/muscle/muscle3.8.31/edgelist.h
diff --git a/src/muscle/muscle3.8.31/src/enumopts.cpp b/src/muscle/muscle3.8.31/enumopts.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/enumopts.cpp
rename to src/muscle/muscle3.8.31/enumopts.cpp
diff --git a/src/muscle/muscle3.8.31/src/enumopts.h b/src/muscle/muscle3.8.31/enumopts.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/enumopts.h
rename to src/muscle/muscle3.8.31/enumopts.h
diff --git a/src/muscle/muscle3.8.31/src/enums.h b/src/muscle/muscle3.8.31/enums.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/enums.h
rename to src/muscle/muscle3.8.31/enums.h
diff --git a/src/muscle/muscle3.8.31/src/enumtostr.cpp b/src/muscle/muscle3.8.31/enumtostr.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/enumtostr.cpp
rename to src/muscle/muscle3.8.31/enumtostr.cpp
diff --git a/src/muscle/muscle3.8.31/src/estring.cpp b/src/muscle/muscle3.8.31/estring.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/estring.cpp
rename to src/muscle/muscle3.8.31/estring.cpp
diff --git a/src/muscle/muscle3.8.31/src/estring.h b/src/muscle/muscle3.8.31/estring.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/estring.h
rename to src/muscle/muscle3.8.31/estring.h
diff --git a/src/muscle/muscle3.8.31/src/fasta.cpp b/src/muscle/muscle3.8.31/fasta.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/fasta.cpp
rename to src/muscle/muscle3.8.31/fasta.cpp
diff --git a/src/muscle/muscle3.8.31/src/fasta2.cpp b/src/muscle/muscle3.8.31/fasta2.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/fasta2.cpp
rename to src/muscle/muscle3.8.31/fasta2.cpp
diff --git a/src/muscle/muscle3.8.31/src/fastclust.cpp b/src/muscle/muscle3.8.31/fastclust.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/fastclust.cpp
rename to src/muscle/muscle3.8.31/fastclust.cpp
diff --git a/src/muscle/muscle3.8.31/src/fastdist.cpp b/src/muscle/muscle3.8.31/fastdist.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/fastdist.cpp
rename to src/muscle/muscle3.8.31/fastdist.cpp
diff --git a/src/muscle/muscle3.8.31/src/fastdistjones.cpp b/src/muscle/muscle3.8.31/fastdistjones.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/fastdistjones.cpp
rename to src/muscle/muscle3.8.31/fastdistjones.cpp
diff --git a/src/muscle/muscle3.8.31/src/fastdistkbit.cpp b/src/muscle/muscle3.8.31/fastdistkbit.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/fastdistkbit.cpp
rename to src/muscle/muscle3.8.31/fastdistkbit.cpp
diff --git a/src/muscle/muscle3.8.31/src/fastdistkmer.cpp b/src/muscle/muscle3.8.31/fastdistkmer.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/fastdistkmer.cpp
rename to src/muscle/muscle3.8.31/fastdistkmer.cpp
diff --git a/src/muscle/muscle3.8.31/src/fastdistmafft.cpp b/src/muscle/muscle3.8.31/fastdistmafft.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/fastdistmafft.cpp
rename to src/muscle/muscle3.8.31/fastdistmafft.cpp
diff --git a/src/muscle/muscle3.8.31/src/fastdistnuc.cpp b/src/muscle/muscle3.8.31/fastdistnuc.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/fastdistnuc.cpp
rename to src/muscle/muscle3.8.31/fastdistnuc.cpp
diff --git a/src/muscle/muscle3.8.31/src/fastscorepath2.cpp b/src/muscle/muscle3.8.31/fastscorepath2.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/fastscorepath2.cpp
rename to src/muscle/muscle3.8.31/fastscorepath2.cpp
diff --git a/src/muscle/muscle3.8.31/src/finddiags.cpp b/src/muscle/muscle3.8.31/finddiags.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/finddiags.cpp
rename to src/muscle/muscle3.8.31/finddiags.cpp
diff --git a/src/muscle/muscle3.8.31/src/finddiagsn.cpp b/src/muscle/muscle3.8.31/finddiagsn.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/finddiagsn.cpp
rename to src/muscle/muscle3.8.31/finddiagsn.cpp
diff --git a/src/muscle/muscle3.8.31/src/gapscoredimer.h b/src/muscle/muscle3.8.31/gapscoredimer.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/gapscoredimer.h
rename to src/muscle/muscle3.8.31/gapscoredimer.h
diff --git a/src/muscle/muscle3.8.31/src/gatest.cpp b/src/muscle/muscle3.8.31/gatest.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/gatest.cpp
rename to src/muscle/muscle3.8.31/gatest.cpp
diff --git a/src/muscle/muscle3.8.31/src/glbalign.cpp b/src/muscle/muscle3.8.31/glbalign.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/glbalign.cpp
rename to src/muscle/muscle3.8.31/glbalign.cpp
diff --git a/src/muscle/muscle3.8.31/src/glbalign352.cpp b/src/muscle/muscle3.8.31/glbalign352.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/glbalign352.cpp
rename to src/muscle/muscle3.8.31/glbalign352.cpp
diff --git a/src/muscle/muscle3.8.31/src/glbaligndiag.cpp b/src/muscle/muscle3.8.31/glbaligndiag.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/glbaligndiag.cpp
rename to src/muscle/muscle3.8.31/glbaligndiag.cpp
diff --git a/src/muscle/muscle3.8.31/src/glbalignla.cpp b/src/muscle/muscle3.8.31/glbalignla.cpp
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similarity index 100%
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rename to src/muscle/muscle3.8.31/pwpath.cpp
diff --git a/src/muscle/muscle3.8.31/src/pwpath.h b/src/muscle/muscle3.8.31/pwpath.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/pwpath.h
rename to src/muscle/muscle3.8.31/pwpath.h
diff --git a/src/muscle/muscle3.8.31/src/readmx.cpp b/src/muscle/muscle3.8.31/readmx.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/readmx.cpp
rename to src/muscle/muscle3.8.31/readmx.cpp
diff --git a/src/muscle/muscle3.8.31/src/realigndiffs.cpp b/src/muscle/muscle3.8.31/realigndiffs.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/realigndiffs.cpp
rename to src/muscle/muscle3.8.31/realigndiffs.cpp
diff --git a/src/muscle/muscle3.8.31/src/realigndiffse.cpp b/src/muscle/muscle3.8.31/realigndiffse.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/realigndiffse.cpp
rename to src/muscle/muscle3.8.31/realigndiffse.cpp
diff --git a/src/muscle/muscle3.8.31/src/redblack.cpp b/src/muscle/muscle3.8.31/redblack.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/redblack.cpp
rename to src/muscle/muscle3.8.31/redblack.cpp
diff --git a/src/muscle/muscle3.8.31/src/refine.cpp b/src/muscle/muscle3.8.31/refine.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/refine.cpp
rename to src/muscle/muscle3.8.31/refine.cpp
diff --git a/src/muscle/muscle3.8.31/src/refinehoriz.cpp b/src/muscle/muscle3.8.31/refinehoriz.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/refinehoriz.cpp
rename to src/muscle/muscle3.8.31/refinehoriz.cpp
diff --git a/src/muscle/muscle3.8.31/src/refinesubfams.cpp b/src/muscle/muscle3.8.31/refinesubfams.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/refinesubfams.cpp
rename to src/muscle/muscle3.8.31/refinesubfams.cpp
diff --git a/src/muscle/muscle3.8.31/src/refinetree.cpp b/src/muscle/muscle3.8.31/refinetree.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/refinetree.cpp
rename to src/muscle/muscle3.8.31/refinetree.cpp
diff --git a/src/muscle/muscle3.8.31/src/refinetreee.cpp b/src/muscle/muscle3.8.31/refinetreee.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/refinetreee.cpp
rename to src/muscle/muscle3.8.31/refinetreee.cpp
diff --git a/src/muscle/muscle3.8.31/src/refinevert.cpp b/src/muscle/muscle3.8.31/refinevert.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/refinevert.cpp
rename to src/muscle/muscle3.8.31/refinevert.cpp
diff --git a/src/muscle/muscle3.8.31/src/refinew.cpp b/src/muscle/muscle3.8.31/refinew.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/refinew.cpp
rename to src/muscle/muscle3.8.31/refinew.cpp
diff --git a/src/muscle/muscle3.8.31/src/releases.txt b/src/muscle/muscle3.8.31/releases.txt
similarity index 100%
rename from src/muscle/muscle3.8.31/src/releases.txt
rename to src/muscle/muscle3.8.31/releases.txt
diff --git a/src/muscle/muscle3.8.31/src/savebest.cpp b/src/muscle/muscle3.8.31/savebest.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/savebest.cpp
rename to src/muscle/muscle3.8.31/savebest.cpp
diff --git a/src/muscle/muscle3.8.31/src/scoredist.cpp b/src/muscle/muscle3.8.31/scoredist.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/scoredist.cpp
rename to src/muscle/muscle3.8.31/scoredist.cpp
diff --git a/src/muscle/muscle3.8.31/src/scoregaps.cpp b/src/muscle/muscle3.8.31/scoregaps.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/scoregaps.cpp
rename to src/muscle/muscle3.8.31/scoregaps.cpp
diff --git a/src/muscle/muscle3.8.31/src/scorehistory.cpp b/src/muscle/muscle3.8.31/scorehistory.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/scorehistory.cpp
rename to src/muscle/muscle3.8.31/scorehistory.cpp
diff --git a/src/muscle/muscle3.8.31/src/scorehistory.h b/src/muscle/muscle3.8.31/scorehistory.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/scorehistory.h
rename to src/muscle/muscle3.8.31/scorehistory.h
diff --git a/src/muscle/muscle3.8.31/src/scoremx.cpp b/src/muscle/muscle3.8.31/scoremx.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/scoremx.cpp
rename to src/muscle/muscle3.8.31/scoremx.cpp
diff --git a/src/muscle/muscle3.8.31/src/scorepp.cpp b/src/muscle/muscle3.8.31/scorepp.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/scorepp.cpp
rename to src/muscle/muscle3.8.31/scorepp.cpp
diff --git a/src/muscle/muscle3.8.31/src/seq.cpp b/src/muscle/muscle3.8.31/seq.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/seq.cpp
rename to src/muscle/muscle3.8.31/seq.cpp
diff --git a/src/muscle/muscle3.8.31/src/seq.h b/src/muscle/muscle3.8.31/seq.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/seq.h
rename to src/muscle/muscle3.8.31/seq.h
diff --git a/src/muscle/muscle3.8.31/src/seqvect.cpp b/src/muscle/muscle3.8.31/seqvect.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/seqvect.cpp
rename to src/muscle/muscle3.8.31/seqvect.cpp
diff --git a/src/muscle/muscle3.8.31/src/seqvect.h b/src/muscle/muscle3.8.31/seqvect.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/seqvect.h
rename to src/muscle/muscle3.8.31/seqvect.h
diff --git a/src/muscle/muscle3.8.31/src/setblosumweights.cpp b/src/muscle/muscle3.8.31/setblosumweights.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/setblosumweights.cpp
rename to src/muscle/muscle3.8.31/setblosumweights.cpp
diff --git a/src/muscle/muscle3.8.31/src/setgscweights.cpp b/src/muscle/muscle3.8.31/setgscweights.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/setgscweights.cpp
rename to src/muscle/muscle3.8.31/setgscweights.cpp
diff --git a/src/muscle/muscle3.8.31/src/setnewhandler.cpp b/src/muscle/muscle3.8.31/setnewhandler.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/setnewhandler.cpp
rename to src/muscle/muscle3.8.31/setnewhandler.cpp
diff --git a/src/muscle/muscle3.8.31/src/spfast.cpp b/src/muscle/muscle3.8.31/spfast.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/spfast.cpp
rename to src/muscle/muscle3.8.31/spfast.cpp
diff --git a/src/muscle/muscle3.8.31/src/sptest.cpp b/src/muscle/muscle3.8.31/sptest.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/sptest.cpp
rename to src/muscle/muscle3.8.31/sptest.cpp
diff --git a/src/muscle/muscle3.8.31/src/Makefile b/src/muscle/muscle3.8.31/src/Makefile
deleted file mode 100644
index 9631dab..0000000
--- a/src/muscle/muscle3.8.31/src/Makefile
+++ /dev/null
@@ -1,11 +0,0 @@
-include ../../../../config/auto.conf
-
-all: muscle install 
-
-muscle:
-	chmod +x ./mk
-	(export CXX=$(CXX) && ./mk)
-
-install:
-	cp muscle $(BINDIR)
-	
diff --git a/src/muscle/muscle3.8.31/src/stabilize.cpp b/src/muscle/muscle3.8.31/stabilize.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/stabilize.cpp
rename to src/muscle/muscle3.8.31/stabilize.cpp
diff --git a/src/muscle/muscle3.8.31/src/subfam.cpp b/src/muscle/muscle3.8.31/subfam.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/subfam.cpp
rename to src/muscle/muscle3.8.31/subfam.cpp
diff --git a/src/muscle/muscle3.8.31/src/subfams.cpp b/src/muscle/muscle3.8.31/subfams.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/subfams.cpp
rename to src/muscle/muscle3.8.31/subfams.cpp
diff --git a/src/muscle/muscle3.8.31/src/svnmods.h b/src/muscle/muscle3.8.31/svnmods.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/svnmods.h
rename to src/muscle/muscle3.8.31/svnmods.h
diff --git a/src/muscle/muscle3.8.31/src/svnversion.h b/src/muscle/muscle3.8.31/svnversion.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/svnversion.h
rename to src/muscle/muscle3.8.31/svnversion.h
diff --git a/src/muscle/muscle3.8.31/src/sw.cpp b/src/muscle/muscle3.8.31/sw.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/sw.cpp
rename to src/muscle/muscle3.8.31/sw.cpp
diff --git a/src/muscle/muscle3.8.31/src/termgaps.cpp b/src/muscle/muscle3.8.31/termgaps.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/termgaps.cpp
rename to src/muscle/muscle3.8.31/termgaps.cpp
diff --git a/src/muscle/muscle3.8.31/src/textfile.cpp b/src/muscle/muscle3.8.31/textfile.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/textfile.cpp
rename to src/muscle/muscle3.8.31/textfile.cpp
diff --git a/src/muscle/muscle3.8.31/src/textfile.h b/src/muscle/muscle3.8.31/textfile.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/textfile.h
rename to src/muscle/muscle3.8.31/textfile.h
diff --git a/src/muscle/muscle3.8.31/src/threewaywt.cpp b/src/muscle/muscle3.8.31/threewaywt.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/threewaywt.cpp
rename to src/muscle/muscle3.8.31/threewaywt.cpp
diff --git a/src/muscle/muscle3.8.31/src/timing.h b/src/muscle/muscle3.8.31/timing.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/timing.h
rename to src/muscle/muscle3.8.31/timing.h
diff --git a/src/muscle/muscle3.8.31/src/tomhydro.cpp b/src/muscle/muscle3.8.31/tomhydro.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/tomhydro.cpp
rename to src/muscle/muscle3.8.31/tomhydro.cpp
diff --git a/src/muscle/muscle3.8.31/src/traceback.cpp b/src/muscle/muscle3.8.31/traceback.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/traceback.cpp
rename to src/muscle/muscle3.8.31/traceback.cpp
diff --git a/src/muscle/muscle3.8.31/src/tracebackopt.cpp b/src/muscle/muscle3.8.31/tracebackopt.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/tracebackopt.cpp
rename to src/muscle/muscle3.8.31/tracebackopt.cpp
diff --git a/src/muscle/muscle3.8.31/src/tracebacksw.cpp b/src/muscle/muscle3.8.31/tracebacksw.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/tracebacksw.cpp
rename to src/muscle/muscle3.8.31/tracebacksw.cpp
diff --git a/src/muscle/muscle3.8.31/src/tree.h b/src/muscle/muscle3.8.31/tree.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/tree.h
rename to src/muscle/muscle3.8.31/tree.h
diff --git a/src/muscle/muscle3.8.31/src/treefrommsa.cpp b/src/muscle/muscle3.8.31/treefrommsa.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/treefrommsa.cpp
rename to src/muscle/muscle3.8.31/treefrommsa.cpp
diff --git a/src/muscle/muscle3.8.31/src/types.h b/src/muscle/muscle3.8.31/types.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/types.h
rename to src/muscle/muscle3.8.31/types.h
diff --git a/src/muscle/muscle3.8.31/src/typetostr.cpp b/src/muscle/muscle3.8.31/typetostr.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/typetostr.cpp
rename to src/muscle/muscle3.8.31/typetostr.cpp
diff --git a/src/muscle/muscle3.8.31/src/unixio.h b/src/muscle/muscle3.8.31/unixio.h
similarity index 100%
rename from src/muscle/muscle3.8.31/src/unixio.h
rename to src/muscle/muscle3.8.31/unixio.h
diff --git a/src/muscle/muscle3.8.31/src/upgma2.cpp b/src/muscle/muscle3.8.31/upgma2.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/upgma2.cpp
rename to src/muscle/muscle3.8.31/upgma2.cpp
diff --git a/src/muscle/muscle3.8.31/src/usage.cpp b/src/muscle/muscle3.8.31/usage.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/usage.cpp
rename to src/muscle/muscle3.8.31/usage.cpp
diff --git a/src/muscle/muscle3.8.31/src/validateids.cpp b/src/muscle/muscle3.8.31/validateids.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/validateids.cpp
rename to src/muscle/muscle3.8.31/validateids.cpp
diff --git a/src/muscle/muscle3.8.31/src/version.txt b/src/muscle/muscle3.8.31/version.txt
similarity index 100%
rename from src/muscle/muscle3.8.31/src/version.txt
rename to src/muscle/muscle3.8.31/version.txt
diff --git a/src/muscle/muscle3.8.31/src/vtml2.cpp b/src/muscle/muscle3.8.31/vtml2.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/vtml2.cpp
rename to src/muscle/muscle3.8.31/vtml2.cpp
diff --git a/src/muscle/muscle3.8.31/src/writescorefile.cpp b/src/muscle/muscle3.8.31/writescorefile.cpp
similarity index 100%
rename from src/muscle/muscle3.8.31/src/writescorefile.cpp
rename to src/muscle/muscle3.8.31/writescorefile.cpp
diff --git a/src/prokov/Makefile b/src/prokov/Makefile
index 2669b78..eedfcf0 100755
--- a/src/prokov/Makefile
+++ b/src/prokov/Makefile
@@ -25,6 +25,3 @@ include ../../config/targets/help.targ
 
 all::
 	$(MAKE) ACTION=$@ _action
-
-clean::
-	$(MAKE) -C lxpack portclean