diff --git a/Makefile.am b/Makefile.am
new file mode 100644
index 0000000..0e6dadb
--- /dev/null
+++ b/Makefile.am
@@ -0,0 +1,18 @@
+# not a GNU package. You can remove this line, if
+# have all needed files, that a GNU package needs
+AUTOMAKE_OPTIONS = foreign
+
+SUBDIRS = src scripts doc 
+
+EXTRA_DIST = README RELEASE Copyright
+
+ACLOCAL_AMFLAGS = -I m4
+
+LN_S=@LN_S@
+
+install-exec-hook:
+	cd ${exec_prefix}/ && \
+	  ${LN_S} -f lib lib64
+
+dist-hook:
+	rm -rf `find $(distdir)/doc -type d -name .svn`
diff --git a/configure.ac b/configure.ac
new file mode 100644
index 0000000..2b20543
--- /dev/null
+++ b/configure.ac
@@ -0,0 +1,191 @@
+AC_INIT([irstlm], [5.80.06])
+AM_INIT_AUTOMAKE([-Wall -Werror foreign])
+AC_PROG_CC
+AC_PROG_CXX
+AC_PROG_LIBTOOL
+AC_CONFIG_HEADERS([config.h])
+AC_CONFIG_MACRO_DIR([m4])
+
+m4_pattern_allow([AM_PROG_AR],[AM_PROG_AR])
+AM_PROG_AR
+
+AC_ARG_ENABLE([doc],
+   [AC_HELP_STRING([--enable-doc|--disable-doc], [Enable or Disable (default) creation of documentation])])
+
+AC_ARG_ENABLE([trace],
+   [AC_HELP_STRING([--enable-trace|--disable-trace], [Enable (default) or Disable trace info at run-time])])
+
+AC_ARG_ENABLE([assert],
+   [AC_HELP_STRING([--enable-assert|--disable-assert], [Enable (default) or Disable assert calls at run-time])])
+
+AC_ARG_ENABLE([debugging],
+   [AC_HELP_STRING([--enable-debugging|--disable-debugging], [Enable or Disable (default) debugging info ("-g -O2")])])
+
+AC_ARG_ENABLE(profiling,
+   [AC_HELP_STRING([--enable-profiling|--disable-profiling], [Enable or Disable (default) profiling info ("-pg")])])
+
+AC_ARG_ENABLE(caching,
+   [AC_HELP_STRING([--enable-caching|--disable-caching], [Enable or Disable (default) internal caches to store probs and other info])])
+
+AC_ARG_ENABLE(output,
+   [AC_HELP_STRING([--enable-output|--disable-output], [Enable (default) or Disable part of the output])])
+
+AC_ARG_ENABLE(interpolatedsearch,
+   [AC_HELP_STRING([--enable-interpolatedsearch|--disable-interpolatedsearch], [Enable or Disable (default) interpolated search for n-grams])])
+
+AC_ARG_ENABLE(optimization,
+   [AC_HELP_STRING([--enable-optimization|--disable-optimization], [Enable or Disable (default) optimization info ("-O3")])])
+
+AC_ARG_ENABLE(cxx0,
+   [AC_HELP_STRING([--enable-cxx0|--disable-cxx0], [Enable or Disable (default) c++0x dialect ("-std=c++0x")])])
+
+AC_ARG_WITH(zlib,
+            [AC_HELP_STRING([--with-zlib=PATH], [(optional) path to zlib])],
+            [with_zlib=$withval],
+            [with_zlib=no]
+           )
+
+AC_ARG_WITH(tracelevel,
+            [AC_HELP_STRING([--with-tracelevel=VAL], [(optional) level of tracing; default 0, tracing disabled])],
+            [with_tracelevel=$withval],
+            [with_tracelevel=0]
+           )
+
+AM_CONDITIONAL([DOC_COMPILATION],false)
+if test "x$enable_doc" = 'xyes'
+then
+    AC_CHECK_TOOL(PDFLATEX,pdflatex,"no")
+    AC_CHECK_TOOL(BIBTEX,bibtex,"no")
+    if test "x$PDFLATEX" != "xno" && test "x$BIBTEX" != "xno"
+    then
+        AM_CONDITIONAL([DOC_COMPILATION],true)
+        AC_MSG_NOTICE([pdflatex and bibtex are available])
+        AC_MSG_NOTICE([documentation will be created])
+    else
+        AC_MSG_NOTICE([either pdflatex or bibtex is not available])
+        AC_MSG_NOTICE([documentation will not be created (default); get it through the website $WEBSITE])
+    fi
+else
+    AC_MSG_NOTICE([documentation will not be created (default); get it through the website $WEBSITE])
+fi
+
+
+#### Use this if you want that the default is yes
+#### if test "x$enable_foo" != 'xno'
+#### Use this if you want that the default is no
+#### if test "x$enable_foo" = 'xyes'
+
+
+if test "x$with_tracelevel" != 'x0'
+then
+if test "x$enable_trace" != 'xno'
+then
+    TRACELEVEL=${with_tracelevel}
+    AC_MSG_NOTICE([trace enabled (default); trace level is $TRACELEVEL])
+else
+    TRACELEVEL=0
+    AC_MSG_NOTICE([trace disabled; trace level is overwritten to $TRACELEVEL; most regression tests will fail])
+fi
+else
+if test "x$enable_trace" != 'xno'
+then
+    TRACELEVEL=1
+    AC_MSG_NOTICE([trace enabled (default); trace level is overwritten to default value $TRACELEVEL])
+else
+    TRACELEVEL=0
+    AC_MSG_NOTICE([trace disabled; trace level is $TRACELEVEL; most regression tests will fail])
+fi
+fi
+CPPFLAGS="$CPPFLAGS -DTRACE_LEVEL=$TRACELEVEL"
+
+if test "x$enable_assert" != 'xno'
+then
+    AC_MSG_NOTICE([assert enabled (default)])
+    CPPFLAGS="$CPPFLAGS -DMY_ASSERT_FLAG" 
+else
+    AC_MSG_NOTICE([assert disabled])
+    CPPFLAGS="$CPPFLAGS -UMY_ASSERT_FLAG" 
+fi
+
+if test "x$enable_debugging" = 'xyes'
+then
+    AC_MSG_NOTICE([generation of debugging symbols enabled, compilation with "-g -O2"])
+    CPPFLAGS="$CPPFLAGS -g -O2"
+else
+    AC_MSG_NOTICE([generation of debugging symbols disabled (default), compilation without "-g", only "-O2"])
+fi
+
+if test "x$enable_profiling" = 'xyes'
+then
+    AC_MSG_NOTICE([profiling enabled, compilation with "-pg"])
+    CPPFLAGS="$CPPFLAGS -pg"
+    LDFLAGS="$LDFLAGS -pg"
+else
+    AC_MSG_NOTICE([profiling disabled (default)])
+fi
+
+if test "x$enable_caching" = 'xyes'
+then
+    AC_MSG_NOTICE([caching enabled])
+    CPPFLAGS="$CPPFLAGS -DPS_CACHE_ENABLE -DLMT_CACHE_ENABLE -DMDIADAPTLM_CACHE_ENABLE";
+    LDFLAGS="$LDFLAGS"
+else
+    AC_MSG_NOTICE([caching disabled (default)])
+fi
+
+if test "x$enable_output" = 'xno'
+then
+    AC_MSG_NOTICE([part of the output on stdout is suppressed])
+    CPPFLAGS="$CPPFLAGS -DOUTPUT_SUPPRESSED";
+    LDFLAGS="$LDFLAGS"
+else
+    AC_MSG_NOTICE([caching disabled (default)])
+fi
+
+if test "x$enable_interpolatedsearch" = 'xyes'
+then
+    AC_MSG_NOTICE([interpolated search enabled])
+    CPPFLAGS="$CPPFLAGS -DINTERP_SEARCH";
+    LDFLAGS="$LDFLAGS"
+else
+    AC_MSG_NOTICE([interpolated search disabled (default)])
+fi
+
+if test "x$enable_optimization" = 'xyes'
+then
+    AC_MSG_NOTICE([optimization enabled, compilation with "-O3"])
+    CPPFLAGS="$CPPFLAGS -O3";
+    LDFLAGS="$LDFLAGS -O3"
+else
+    AC_MSG_NOTICE([optimization disabled (default)])
+fi
+
+if test "x$enable_cxx0" != 'xno'
+then
+    AC_MSG_NOTICE([c++x0 dialect is enabled (default), compilation with "-DHAVE_CXX0 -std=c++0x "])
+    CPPFLAGS="$CPPFLAGS -DHAVE_CXX0 -std=c++0x";
+else
+    AC_MSG_NOTICE([c++x0 dialect is disabled, compilation without "-std=c++0x" and with "-UHAVE_CXX0"])
+    CPPFLAGS="$CPPFLAGS -UHAVE_CXX0";
+fi
+
+if test "x$with_zlib" != 'xno'
+then
+  CPPFLAGS="$CPPFLAGS -I${with_zlib}/include"
+  LDFLAGS="$LDFLAGS -L${with_zlib}/lib"
+fi
+
+LIBS="$LIBS -lz"
+
+AC_CONFIG_FILES([
+Makefile
+src/Makefile
+scripts/Makefile
+doc/Makefile
+])
+
+AC_SUBST(transform,'s/_lm/-lm/')
+
+AC_OUTPUT()
+
+AC_MSG_NOTICE([The software will be installed into $prefix])
diff --git a/doc/Makefile.am b/doc/Makefile.am
new file mode 100644
index 0000000..a3d449b
--- /dev/null
+++ b/doc/Makefile.am
@@ -0,0 +1,23 @@
+documentationdir = @prefix@/doc
+
+if DOC_COMPILATION
+
+irstlm-manual.pdf: irstlm-manual.tex
+	pdflatex irstlm-manual ; \
+	bibtex irstlm-manual ; \
+	pdflatex irstlm-manual ; \
+	pdflatex irstlm-manual ; \
+	rm *.aux *.log *.bbl *.blg
+
+clean-local:
+	rm -rf irstlm-manual.pdf
+
+all: irstlm-manual.pdf
+ 
+dist_documentation_SCRIPTS = irstlm-manual.pdf
+
+endif
+
+EXTRA_DIST = irstlm-manual.tex 
+
+
diff --git a/regenerate-makefiles.sh b/regenerate-makefiles.sh
new file mode 100755
index 0000000..68152b6
--- /dev/null
+++ b/regenerate-makefiles.sh
@@ -0,0 +1,84 @@
+#!/bin/bash
+
+# NOTE:
+# Versions 1.9 (or higher) of aclocal and automake are required.
+# Version 2.59 (or higher) of autoconf is required.
+
+# For Mac OSX users:
+# Standard distribution usually includes versions 1.6 for aclocal and automake.
+# Get versions 1.9 or higher
+# Set the following variable to the correct paths
+#ACLOCAL="/path/to/aclocal-1.9"
+#AUTOMAKE="/path/to/automake-1.9"
+
+force=$1;
+# set parameter force to the value "--force" if you want to recreate all links to the autotools
+
+die () {
+  echo "$@" >&2
+  exit 1
+}
+
+if [ -z "$ACLOCAL" ]
+then
+    ACLOCAL=`which aclocal`
+fi
+
+if [ -z "$AUTOMAKE" ]
+then
+    AUTOMAKE=`which automake`
+fi
+
+if [ -z "$AUTORECONF" ]
+then
+    AUTORECONF=`which autoreconf`
+fi
+
+if [ -z "$AUTOCONF" ]
+then
+    AUTOCONF=`which autoconf`
+fi
+
+if [ -z "$LIBTOOLIZE" ]
+then
+    LIBTOOLIZE=`which libtoolize`
+
+    if [ -z "$LIBTOOLIZE" ]
+    then
+        LIBTOOLIZE=`which glibtoolize`
+    fi
+fi
+
+if [ ! -d m4 ] ;
+then
+mkdir m4
+fi
+
+echo "Calling $AUTORECONF"
+$AUTORECONF
+
+ret=$?
+
+if [ $ret -ne 0 ] ; then
+echo "autoreconf FAILED"
+echo "trying '$LIBTOOLIZE --force; $AUTOMAKE --add-missing ; $AUTORECONF'"
+$LIBTOOLIZE --force
+$AUTOMAKE  --add-missing
+$AUTORECONF
+if [ ! -e config.guess ] ; then 
+$AUTOMAKE  --add-missing
+$AUTORECONF
+fi
+fi
+
+#echo "Calling $LIBTOOLIZE $force"
+#$LIBTOOLIZE $force || die "libtoolize failed"
+
+#echo "Calling $ACLOCAL..."
+#$ACLOCAL -I m4 || die "aclocal failed"
+
+#echo "Calling $AUTOCONF..."
+#$AUTOCONF || die "autoconf failed"
+
+#echo "Calling $AUTOMAKE --add-missing..."
+#$AUTOMAKE --add-missing || die "automake failed"
diff --git a/scripts/Makefile.am b/scripts/Makefile.am
new file mode 100644
index 0000000..6893b01
--- /dev/null
+++ b/scripts/Makefile.am
@@ -0,0 +1,9 @@
+wrapperbindir = @prefix@/bin
+
+dist_wrapperbin_SCRIPTS = \
+add-start-end.sh build-lm-qsub.sh build-lm.sh rm-start-end.sh split-ngt.sh mdtsel.sh \
+build-sublm.pl goograms2ngrams.pl lm-stat.pl merge-sublm.pl ngram-split.pl sort-lm.pl split-dict.pl \
+plsa.sh qplsa.sh
+
+EXTRA_DIST = wrapper
+
diff --git a/src/Makefile.am b/src/Makefile.am
new file mode 100644
index 0000000..1f8a065
--- /dev/null
+++ b/src/Makefile.am
@@ -0,0 +1,97 @@
+lib_LTLIBRARIES = libirstlm.la
+
+AM_CXXFLAGS = -isystem/usr/include -W -Wall -ffor-scope -D_FILE_OFFSET_BITS=64 -D_LARGE_FILES $(BOOST_CPPFLAGS) -DMYCODESIZE=3
+
+libirstlm_ladir = ${includedir}
+
+libirstlm_la_HEADERS = \
+  cmd.h \
+  thpool.h \
+  dictionary.h \
+  gzfilebuf.h \
+  htable.h \
+  index.h \
+  lmContainer.h \
+  lmclass.h \
+  lmmacro.h \
+  lmtable.h \
+  lmInterpolation.h \
+  mempool.h \
+  mfstream.h \
+  n_gram.h \
+  ngramcache.h \
+  ngramtable.h \
+  timer.h \
+  util.h \
+  crc.h \
+  interplm.h \
+  linearlm.h \
+  mdiadapt.h \
+  mixture.h \
+  normcache.h \
+  shiftlm.h \
+  cplsa.h \
+  cswam.h \
+  doc.h
+
+libirstlm_la_SOURCES = \
+  cmd.c \
+  thpool.c \
+  dictionary.cpp \
+  htable.cpp \
+  lmContainer.cpp \
+  lmclass.cpp \
+  lmmacro.cpp \
+  lmtable.cpp \
+  lmInterpolation.cpp \
+  mempool.cpp \
+  mfstream.cpp \
+  n_gram.cpp \
+  ngramcache.cpp \
+  ngramtable.cpp \
+  timer.cpp \
+  util.cpp \
+  crc.cpp \
+  interplm.cpp \
+  linearlm.cpp \
+  mdiadapt.cpp \
+  mixture.cpp \
+  normcache.cpp \
+  shiftlm.cpp \
+  cplsa.cpp \
+  cswam.cpp \
+  doc.cpp
+
+CLEANFILES = $(BUILT_SOURCES)
+
+libirstlm_la_LIBADD = $(BOOST_LDFLAGS) $(BOOST_THREAD_LIB)
+
+LDADD = -lirstlm -lpthread
+DEPENDENCIES = libirstlm.la
+
+bin_PROGRAMS = dict ngt dtsel compile-lm interpolate-lm prune-lm quantize-lm prune-lm score-lm tlm plsa verify-caching cswa
+
+dict_SOURCES = dict.cpp
+dict_DEPENDENCIES = $(DEPENDENCIES)
+ngt_SOURCES = ngt.cpp
+ngt_DEPENDENCIES = $(DEPENDENCIES)
+dtsel_SOURCES = dtsel.cpp
+dtsel_DEPENDENCIES = $(DEPENDENCIES)
+compile_lm_SOURCES = compile-lm.cpp
+compile_lm_DEPENDENCIES = $(DEPENDENCIES)
+interpolate_lm_SOURCES = interpolate-lm.cpp
+interpolate_lm_DEPENDENCIES = $(DEPENDENCIES)
+prune_lm_SOURCES = prune-lm.cpp
+prune_lm_DEPENDENCIES = $(DEPENDENCIES)
+quantize_lm_SOURCES = quantize-lm.cpp
+quantize_lm_DEPENDENCIES = $(DEPENDENCIES)
+score_lm_SOURCES = score-lm.cpp
+score_lm_DEPENDENCIES = $(DEPENDENCIES)
+tlm_SOURCES = tlm.cpp
+tlm_DEPENDENCIES = $(DEPENDENCIES)
+plsa_SOURCES = plsa.cpp
+plsa_DEPENDENCIES = $(DEPENDENCIES)
+verify_caching_SOURCES = verify-caching.cpp
+verify_caching_DEPENDENCIES = $(DEPENDENCIES)
+cswa_SOURCES = cswa.cpp
+cswa_DEPENDENCIES = $(DEPENDENCIES)