--- /dev/null
+# Replaces squids own automake files
+#
+# 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 = COPYRIGHT LICENSE 00README clustalo.README squid-1.9g.tar.gz
+#LDADD =
+
+# need DCLUSTALO here to enable Clustal specific squid patches
+# CLUSTALO is also defined in ../config.h which is included by squid.h
+# but some files do not include squid.h
+AM_CFLAGS = -DCLUSTALO -DSRE_STRICT_ANSI @AM_CFLAGS@
+
+noinst_LTLIBRARIES = libsquid.la
+
+libsquid_la_SOURCES = a2m.c aligneval.c alignio.c \
+ clustal.c cluster.c \
+ dayhoff.c \
+ eps.c \
+ file.c \
+ getopt.c gki.c gki.h gsi.c gsi.h gsi64.c gsi64.h \
+ hsregex.c \
+ iupac.c \
+ msa.c msa.h msf.c \
+ phylip.c \
+ revcomp.c rk.c rk.h \
+ selex.c seqencode.c shuffle.c sqerror.c sqfuncs.h sqio.c squid.h squidcore.c \
+ sre_ctype.c sre_math.c sre_random.c sre_random.h sre_string.c \
+ ssi.c ssi.h stack.c stockholm.c stockholm.h stopwatch.c stopwatch.h \
+ translate.c types.c vectorops.c \
+ vectorops.h version.h \
+ weight.c
+
+library_includedir=$(includedir)/clustalo/squid
+
+library_include_HEADERS = gki.h gsi64.h msa.h rk.h \
+ squid.h stopwatch.h sqfuncs.h \
+ sre_random.h ssi.h stockholm.h \
+ vectorops.h version.h
+
+