--- /dev/null
+# Some useful automake documentation:
+# http://www.openismus.com/documents/linux/automake/automake.shtml
+# http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
+
+#SUBDIRS =
+#EXTRA_DIST =
+# LDADD = foofiles/libfoo.a
+
+AM_CXXFLAGS = -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 @OPENMP_CXXFLAGS@ @AM_CXXFLAGS@
+
+noinst_LTLIBRARIES = libhhalign.la
+
+libhhalign_la_SOURCES = hhalign.cpp hhalign.h \
+ hash-C.h hash.h hhdecl-C.h hhfunc-C.h hhfunc.h \
+ hhmatrices-C.h hhutil-C.h \
+ hhalignment-C.h hhalignment.h \
+ hhfullalignment-C.h hhfullalignment.h \
+ hhhalfalignment-C.h hhhalfalignment.h \
+ hhhit-C.h hhhit.h hhhitlist-C.h hhhitlist.h \
+ hhhmm-C.h hhhmm.h \
+ util-C.h list-C.h list.h \
+ general.h
+
+library_includedir=$(includedir)/clustalo/hhalign
+
+library_include_HEADERS = general.h hhfunc.h