--- a/GEMBASSY-1.0.3/src/Makefile.am	Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,164 +0,0 @@
-## Process this file with automake to produce Makefile.in
-
-if LOCALLINK
-INCLUDES = -I../include -I../../../nucleus -I../../../ajax/pcre \
-	-I../../../ajax/expat -I../../../ajax/zlib \
-	-I../../../ajax/core -I../../../ajax/graphics \
-	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
-	-I../../../ajax/acd -I../../../plplot -I../gsoap
-else
-INCLUDES = -I../include -I${embprefix}/include -I${embprefix}/include/eplplot -I${embprefix}/include/epcre -I${embprefix}/include/ezlib -I../gsoap
-endif
-
-if ISSHARED
-if ISAIXIA64
-if LOCALLINK
-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L../../../plplot/.libs \
--L../../../ajax/pcre/.libs -L../../../ajax/expat/.libs \
--L../../../ajax/zlib/.libs -L../../../ajax/core/.libs \
--L../../../ajax/graphics/.libs -L../../../ajax/ensembl/.libs \
--L../../../ajax/ajaxdb/.libs -L../../../ajax/acd/.libs \
--L../../../nucleus/.libs \
--lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -leexpat -lepcre \
--lezlib -leplplot
-else
-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
--lajaxdb -lensembl -lajaxg -lajax -leexpat -lepcre -lezlib -leplplot
-endif
-endif
-endif
-
-AM_CFLAGS =  $(AIX_CFLAGS) $(WARN_CFLAGS) $(DEVWARN_CFLAGS)
-
-## To add programs
-## Add the program binary name to bin_PROGRAMS
-## (using \ as a continuation character for multiple lines)
-##
-## And add a programname_SOURCES line to define the source files
-## to be compiled and linked
-##
-## make will compile and link the program
-## make install will copy the program to the install directory
-
-bin_PROGRAMS = genret \
-               gaaui\
-               gaminoinfo\
-               gb1\
-               gb2\
-               gbasecounter\
-               gbaseentropy\
-               gbaseinformationcontent\
-               gbaserelativeentropy\
-               gbasezvalue\
-	       gbui\
-               gcai\
-               gcbi\
-               gcgr\
-               gcircularmap\
-               gcodoncompiler\
-               gconsensusz\
-               gdeltaenc\
-               gdeltagcskew\
-               gdinuc\
-               gdistincc\
-               gdnawalk\
-               genc\
-               gentrez\
-               gew\
-               gfindoriter\
-               gfop\
-               ggcsi\
-               ggcskew\
-               ggcwin\
-               ggeneskew\
-               ggenomicskew\
-               ggenomemap3\
-               gicdi\
-               gkmertable\
-               gldabias\
-               gnucleotideperiodicity\
-	       goligomercounter\
-	       goligomersearch\
-               gp2\
-               gpalindrome\
-               gphx\
-               gqueryarm\
-               gquerystrand\
-               greporiter\
-               gsvalue\
-               gscs\
-               gseq2png\
-               gseqinfo\
-               gshuffleseq\
-               gsignature\
-               gviewcds\
-               gwvalue
-
-genret_SOURCES                  = genret.c
-gaaui_SOURCES                   = gaaui.c
-gaminoinfo_SOURCES              = gaminoinfo.c
-gb1_SOURCES                     = gb1.c
-gb2_SOURCES                     = gb2.c
-gbasecounter_SOURCES            = gbasecounter.c
-gbaseentropy_SOURCES            = gbaseentropy.c
-gbaseinformationcontent_SOURCES = gbaseinformationcontent.c
-gbaserelativeentropy_SOURCES    = gbaserelativeentropy.c
-gbasezvalue_SOURCES             = gbasezvalue.c
-gbui_SOURCES                    = gbui.c
-gcai_SOURCES                    = gcai.c
-gcbi_SOURCES                    = gcbi.c
-gcgr_SOURCES                    = gcgr.c
-gcircularmap_SOURCES            = gcircularmap.c
-gcodoncompiler_SOURCES          = gcodoncompiler.c
-gconsensusz_SOURCES             = gconsensusz.c
-gdeltaenc_SOURCES               = gdeltaenc.c
-gdeltagcskew_SOURCES            = gdeltagcskew.c
-gdistincc_SOURCES               = gdistincc.c
-gdinuc_SOURCES                  = gdinuc.c
-gdnawalk_SOURCES                = gdnawalk.c
-genc_SOURCES                    = genc.c
-gentrez_SOURCES                 = gentrez.c
-gew_SOURCES                     = gew.c
-gfindoriter_SOURCES             = gfindoriter.c
-gfop_SOURCES                    = gfop.c
-ggcsi_SOURCES                   = ggcsi.c
-ggcwin_SOURCES                  = ggcwin.c
-ggeneskew_SOURCES               = ggeneskew.c
-ggenomicskew_SOURCES            = ggenomicskew.c
-ggenomemap3_SOURCES             = ggenomemap3.c
-gicdi_SOURCES                   = gicdi.c
-gkmertable_SOURCES              = gkmertable.c
-gldabias_SOURCES                = gldabias.c
-gnucleotideperiodicity_SOURCES  = gnucleotideperiodicity.c
-goligomercounter_SOURCES        = goligomercounter.c
-goligomersearch_SOURCES         = goligomersearch.c
-gp2_SOURCES                     = gp2.c
-gpalindrome_SOURCES             = gpalindrome.c
-gphx_SOURCES                    = gphx.c
-gqueryarm_SOURCES               = gqueryarm.c
-gquerystrand_SOURCES            = gquerystrand.c
-greporiter_SOURCES              = greporiter.c
-gsvalue_SOURCES                 = gsvalue.c
-gscs_SOURCES                    = gscs.c
-gseq2png_SOURCES                = gseq2png.c
-gseqinfo_SOURCES                = gseqinfo.c
-gshuffleseq_SOURCES             = gshuffleseq.c
-gsignature_SOURCES              = gsignature.c
-gviewcds_SOURCES                = gviewcds.c
-gwvalue_SOURCES                 = gwvalue.c
-
-if LOCALLINK
-LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
-	../../../ajax/ajaxdb/libajaxdb.la \
-	../../../ajax/ensembl/libensembl.la \
-	../../../ajax/graphics/libajaxg.la \
-	../../../ajax/core/libajax.la \
-	../../../ajax/zlib/libezlib.la \
-	../../../ajax/expat/libeexpat.la \
-	../../../ajax/pcre/libepcre.la \
-	../../../plplot/libeplplot.la \
-        $(XLIB)
-else
-LDADD = -L${embprefix}/lib -L../include -lnucleus -lacd -lajaxdb -lensembl \
-        -lajaxg -lajax -leexpat -lepcre -lezlib -leplplot $(XLIB)
-endif