--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clustalomega/clustal-omega-0.2.0/src/squid/Makefile.am	Tue Jun 07 17:04:25 2011 -0400
@@ -0,0 +1,43 @@
+# 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
+
+