diff --git a/configure.ac b/configure.ac
index 68453ef..3ecfd21 100644
--- a/configure.ac
+++ b/configure.ac
@@ -28,13 +28,11 @@ AC_CHECK_FUNCS([floor memset clock pow sqrt strchr strdup strtol strtoul])
 dnl 1) threads options
 
 dnl abc) : with-threads option
-AC_ARG_WITH(
-	threads,
-	[  --with-threads          compile with all threads],
-	[threads="yes"],
-	[threads="no"])
+AC_ARG_ENABLE(
+	[threads],
+	AS_HELP_STRING([--enable-threads], [compile with all threads]))
 
-if test "$threads" = "yes"; then
+AS_IF([test "x$enable_threads" = "xyes"], [
   AC_MSG_RESULT(detected cpu parameter: threads);
  
   dnl pthread library here ? (UNIX system)
@@ -46,167 +44,25 @@ if test "$threads" = "yes"; then
     AC_MSG_RESULT(yes)
     AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer])
        CFLAGS=" $CFLAGS -DTHREAD_ASSEMBLE_ALIGN -DTHREAD_FORWARD_REVERSE -DTHREAD_QUERY_CHUNK "
-       LDFLAGS="$LDFLAGS -lpthread"
+       LIBS="$LIBS -lpthread"
   else
     AC_MSG_RESULT(no : disabling \"--with-threads\" parameter)
   fi
-
-else
-   if test -s /proc/cpuinfo; then
-      AC_MSG_CHECKING(for multi-processor)
-      dnl Multithread advice
-      if test `grep -c '^processor' /proc/cpuinfo` -gt 2; then
-         AC_MSG_RESULT(yes) 
-         AC_MSG_RESULT(- try \"configure --with-threads\")
-      else
-         AC_MSG_RESULT(no)
-      fi;
-   fi;
-fi
-
-
-
-
-
-dnl a) : with-thread-fr option
-AC_ARG_WITH(
-	thread-fr,
-	[  --with-thread-fr        compile with two separate threads for Forward and Reverse sequence],
-	[thread_forward_reverse="yes"],
-	[thread_forward_reverse="no"])
-
-if test "$thread_forward_reverse" = "yes"; then
-  AC_MSG_RESULT(detected cpu parameter: thread-fr);
- 
-  dnl pthread library here ? (UNIX system)
-  AC_MSG_CHECKING(for pthread lib)
-  AC_CHECK_LIB(pthread, pthread_create,
-	[have_pthread="yes"],
-	[have_pthread="no"])
-  if test "$have_pthread" = "yes"; then
-    AC_MSG_RESULT(yes)
-    AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer])
-       CFLAGS=" $CFLAGS -DTHREAD_FORWARD_REVERSE "
-       LDFLAGS="$LDFLAGS -lpthread"  
-  else
-    AC_MSG_RESULT(no : disabling \"--with-thread-fr\" parameter)
-  fi
-
-else
-   if test -s /proc/cpuinfo; then
-      AC_MSG_CHECKING(for multi-processor)
-      dnl Multithread advice
-      if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then
-         AC_MSG_RESULT(yes) 
-         AC_MSG_RESULT(- try \"configure --with-thread-fr\")
-      else
-         AC_MSG_RESULT(no)
-      fi;
-   fi;
-fi
-
-
-
-
-
-dnl b) : with-thread-aa option
-AC_ARG_WITH(
-	thread-aa,
-	[  --with-thread-aa        compile with two separate threads for Assemble and Align steps],
-	[thread_assemble_align="yes"],
-	[thread_assemble_align="no"])
-
-if test "$thread_assemble_align" = "yes"; then
-  AC_MSG_RESULT(detected cpu parameter: thread-aa);
- 
-  dnl pthread library here ? (UNIX system)
-  AC_MSG_CHECKING(for pthread lib)
-  AC_CHECK_LIB(pthread, pthread_create,
-	[have_pthread="yes"],
-	[have_pthread="no"])
-  if test "$have_pthread" = "yes"; then
-    AC_MSG_RESULT(yes)
-    AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer])
-       CFLAGS=" $CFLAGS -DTHREAD_ASSEMBLE_ALIGN "
-       LDFLAGS="$LDFLAGS -lpthread"  
-  else
-    AC_MSG_RESULT(no : disabling \"--with-thread-aa\" parameter)
-  fi
-
-else
-   if test -s /proc/cpuinfo; then
-      AC_MSG_CHECKING(for multi-processor)
-      dnl Multithread advice
-      if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then
-         AC_MSG_RESULT(yes) 
-         AC_MSG_RESULT(- try \"configure --with-thread-aa\")
-      else
-         AC_MSG_RESULT(no)
-      fi;
-   fi;
-fi
-
-
-dnl c) : with-thread-qc option
-AC_ARG_WITH(
-	thread-qc,
-	[  --with-thread-qc        compile with threads for the query chunks],
-	[thread_query_chunk="yes"],
-	[thread_query_chunk="no"])
-
-if test "$thread_query_chunk" = "yes"; then
-  AC_MSG_RESULT(detected cpu parameter: thread-qc);
- 
-  dnl pthread library here ? (UNIX system)
-  AC_MSG_CHECKING(for pthread lib)
-  AC_CHECK_LIB(pthread, pthread_create,
-	[have_pthread="yes"],
-	[have_pthread="no"])
-  if test "$have_pthread" = "yes"; then
-    AC_MSG_RESULT(yes)
-    AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer])
-       CFLAGS=" $CFLAGS -DTHREAD_QUERY_CHUNK "
-       LDFLAGS="$LDFLAGS -lpthread"  
-  else
-    AC_MSG_RESULT(no : disabling \"--with-thread-qc\" parameter)
-  fi
-
-else
-   if test -s /proc/cpuinfo; then
-      AC_MSG_CHECKING(for multi-processor)
-      dnl Multithread advice
-      if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then
-         AC_MSG_RESULT(yes) 
-         AC_MSG_RESULT(- try \"configure --with-thread-qc\")
-      else
-         AC_MSG_RESULT(no)
-      fi;
-   fi;
-fi
-
-
-
+])
 
 dnl 2) : low-memory option
-AC_ARG_WITH(
-	low-memory,
-	[  --with-low-memory       use less memory, but can miss some repeats],
-	[low_memory="yes"],
-	[low_memory="no"])
+AC_ARG_ENABLE(
+	[lowmemory],
+	AS_HELP_STRING([--enable-lowmemory], [use less memory, but can miss some repeats]))
 
-if test "$low_memory" = "yes"; then
+AS_IF([test "x$enable_lowmemory" = "xyes"], [
    AC_MSG_RESULT(detected memory parameter: low memory);
    CFLAGS=" $CFLAGS -DLOW_MEMORY "
-else
-   AC_MSG_RESULT(detected memory parameter : plain memory) 
-fi
-
-
-CFLAGS="$CFLAGS -O3 -Wall -ansi -pedantic -funroll-loops -pipe -fomit-frame-pointer "
-LDFLAGS="$LDFLAGS -lm"
+])
 
 AC_SUBST(CFLAGS)
 AC_SUBST(LDFLAGS)
+
 AM_WITH_DMALLOC
 AM_INIT_AUTOMAKE
 AC_CONFIG_FILES([Makefile
diff --git a/src/Makefile.am b/src/Makefile.am
index e456f94..8d90ca9 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -6,3 +6,4 @@
 bin_PROGRAMS = yass
 yass_SOURCES = align.c assemble.c avl.c display.c global_var.c hash.c kword.c list.c main.c prdyn.c proba.c red_black.c regroup.c threads.c tuple.c util.c \
                align.h assemble.h avl.h display.h global_var.h hash.h kword.h list.h        prdyn.h proba.h red_black.h regroup.h threads.h tuple.h util.h
+yass_LDADD = -lm