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MKDIR_P = @MKDIR_P@
MPICC = @MPICC@
MPIFLAGS = @MPIFLAGS@
MPIINC = @MPIINC@
MPILIBDIR = @MPILIBDIR@
MPIRUN = @MPIRUN@
MPITYPE = @MPITYPE@
MPI_CMD = @MPI_CMD@
NEWS_URL = @NEWS_URL@
NM = @NM@
NMEDIT = @NMEDIT@
NOTICES_URL = @NOTICES_URL@
OBJDUMP = @OBJDUMP@
OBJEXT = @OBJEXT@
OPAL_DEPLOY = @OPAL_DEPLOY@
OPAL_URL = @OPAL_URL@
OPT_FLAGS = @OPT_FLAGS@
OTOOL = @OTOOL@
OTOOL64 = @OTOOL64@
PACKAGE = @PACKAGE@
PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
PACKAGE_NAME = @PACKAGE_NAME@
PACKAGE_STRING = @PACKAGE_STRING@
PACKAGE_TARNAME = @PACKAGE_TARNAME@
PACKAGE_URL = @PACKAGE_URL@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
PERL = @PERL@
PREV_URL = @PREV_URL@
PREV_VER = @PREV_VER@
PYTHON = @PYTHON@
PYTHON3 = @PYTHON3@
QUOTA = @QUOTA@
RANLIB = @RANLIB@
SED = @SED@
SENDMAIL = @SENDMAIL@
SET_MAKE = @SET_MAKE@
SHELL = @SHELL@
STRIP = @STRIP@
URL = @URL@
VERSION = @VERSION@
WEBSERVICE = @WEBSERVICE@
XML2_CONFIG = @XML2_CONFIG@
XSLT_CONFIG = @XSLT_CONFIG@
abs_builddir = @abs_builddir@
abs_srcdir = @abs_srcdir@
abs_top_builddir = @abs_top_builddir@
abs_top_srcdir = @abs_top_srcdir@
ac_ct_AR = @ac_ct_AR@
ac_ct_CC = @ac_ct_CC@
ac_ct_DUMPBIN = @ac_ct_DUMPBIN@
am__include = @am__include@
am__leading_dot = @am__leading_dot@
am__quote = @am__quote@
am__tar = @am__tar@
am__untar = @am__untar@
bindir = @bindir@
build = @build@
build_alias = @build_alias@
build_cpu = @build_cpu@
build_os = @build_os@
build_vendor = @build_vendor@
builddir = @builddir@
datadir = @datadir@
datarootdir = @datarootdir@
docdir = @docdir@
dvidir = @dvidir@
exec_prefix = @exec_prefix@
host = @host@
host_alias = @host_alias@
host_cpu = @host_cpu@
host_os = @host_os@
host_vendor = @host_vendor@
htmldir = @htmldir@
includedir = @includedir@
infodir = @infodir@
install_sh = @install_sh@
libdir = @libdir@
libexecdir = @libexecdir@
localedir = @localedir@
localstatedir = @localstatedir@
mandir = @mandir@
mkdir_p = @mkdir_p@
oldincludedir = @oldincludedir@
pdfdir = @pdfdir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
sysconfdir = @sysconfdir@
target_alias = @target_alias@
top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
ARCHIVE_REVISION = $(shell cat ../ARCHIVE_REVISION)
ARCHIVE_DATE = $(shell cat ../ARCHIVE_DATE)
SUBDIRS = filters libxml2 libxslt libexslt . parallel
BUILT_SOURCES = dir.h projrel.h
OBSOLETE_PROGS = \
  beadstring \
  draw-mhmm \
  mhmm \
  mhmme \
  mhmms \
  mhmmscan \
  shadow \
  tree

USELESS_PROGS = \
  alph-in \
  clustalw-io \
  fasta-io \
  mhmm-io \
  xlate-in

PROGS = \
  alphtype \
  ama \
  ame \
  ceqlogo \
  centrimo \
  clustalw2fasta \
  clustalw2phylip \
  compute-prior-dist \
  compute-uniform-priors \
  create-priors \
  fasta-get-markov \
  fasta-shuffle-letters \
  fimo \
  fisher_exact \
  fitevd \
  gendb \
  getsize \
  glam2 \
  glam2format \
  glam2mask \
  glam2scan \
  gomo \
  gomo_highlight \
  import-html-template \
  llr \
  mast \
  mcast \
  meme2alph \
  meme2images \
  meme2meme \
  meme-get-motif \
  motif-shuffle-columns \
  motiph \
  pmp_bf \
  ramen \
  spamo \
  tomtom \
  qvalue \
  ranksum_test \
  reconcile-tree-alignment \
  reduce-alignment \
  remove-alignment-gaps \
  xsltproc_lite

noinst_LTLIBRARIES = libcommon.la

# Build the source common to all the binaries into a library
libcommon_la_CFLAGS = \
	-fno-strict-aliasing \
	$(AM_CFLAGS) \
	$(LIBXML2_CFLAGS) \
	$(LIBXSLT_CFLAGS) \
	$(LIBEXSLT_CFLAGS)

libcommon_la_LIBADD = \
	$(LIBXML2_LIBS) \
	$(LIBXSLT_LIBS) \
	$(LIBEXSLT_LIBS) \
	-lm

libcommon_la_SOURCES = \
  alignment.c \
  alph-in.c \
  alphabet.c \
  array.c \
  array-list.c \
  binary-search.c \
  binomial.c \
  build-hmm.c \
  buffer.c \
  ceqlogo.c \
  cisml.c \
  cisml-sax.c \
  clustalw-io.c \
  dp.c \
  dreme-sax.c \
  eps2png.c \
  empirical-qvalue.c \
  evomodel.c \
  fasta-io.c \
  fitevd.c \
  gendb.c \
  hash_table.c \
  heap.c \
  html-data.c \
  html-monolith.c \
  io.c \
  json-checker.c \
  json-reader.c \
  json-writer.c \
  karlin.c \
  linked-list.c \
  log-hmm.c \
  logodds.c \
  mast-util.c \
  match.c \
  matrix.c \
  mcast-match.c \
  meme-sax.c \
  metameme.c \
  mhmm.c \
  mhmms.c \
  mhmmscan.c \
  mhmm-state.c \
  motif-in.c \
  motif-in-common.c \
  motif-in-dreme-xml.c \
  motif-in-meme-html.c \
  motif-in-meme-json.c \
  motif-in-meme-text.c \
  motif-in-meme-xml.c \
  motif.c \
  motif_regexp.c \
  motifs.c \
  motiph-scoring.c \
  mtwist.c \
  object-list.c \
  order.c \
  data-block.c \
  data-block-reader.c \
  parser-message.c \
  prealigned-io.c \
  prior-reader-from-psp.c \
  prior-reader-from-wig.c \
  prior-dist.c \
  pssm.c \
  pssm-distr.c \
  qvalue.c \
  ranksum_test.c \
  ranksum_test.h \
  rdb-matrix.c \
  read-mhmm.c \
  read_sequence.c \
  red-black-tree.c \
  regex-utils.c \
  regress.c \
  reservoir.c \
  sax-parser-utils.c \
  scanned-sequence.c \
  scored-sites.c \
  seq.c \
  seq-reader-from-fasta.c \
  simple-getopt.c \
  spearman-rank-correlation.c \
  spearman-rank-correlation.h \
  string-builder.c \
  string-list.c \
  string-match.c \
  subst-matrix.c \
  substmatrix-table.c \
  transfac.c \
  tree.c \
  utils.c \
  wiggle-reader.c \
  write-mhmm.c \
  xlate-in.c \
  xml-out.c \
  xml-util.c

alphtype_CFLAGS = $(AM_CFLAGS)
alphtype_LDADD = libcommon.la
alphtype_SOURCES = alphtype.c
alph_in_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(OPENMP_CFLAGS)
alph_in_LDADD = libcommon.la $(LIBXML2_LIBS)
alph_in_SOURCES = alph-in.c parser-message.c

# Describe the source files and build options for each executable
ama_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(OPENMP_CFLAGS)
ama_LDADD = libcommon.la $(LIBXML2_LIBS)
ama_SOURCES = \
  ama.c

ame_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS)
ame_SOURCES = ame.c ramen_scan.c fisher_exact.c
ame_LDADD = libcommon.la $(LIBXML2_LIBS) -lm 
beadstring_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS)
beadstring_LDADD = libcommon.la $(LIBXML2_LIBS) $(LIBXSLT_LIBS)
beadstring_SOURCES = beadstring.c
centrimo_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS)
centrimo_LDADD = libcommon.la $(LIBXML2_LIBS)
centrimo_SOURCES = centrimo.c fisher_exact.c
ceqlogo_CFLAGS = -DCL_MAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS)
ceqlogo_LDADD = libcommon.la $(LIBXML2_LIBS)
ceqlogo_SOURCES = ceqlogo.c
clustalw_io_CFLAGS = -DMAIN $(AM_CFLAGS)
clustalw_io_LDADD = libcommon.la
clustalw_io_SOURCES = clustalw-io.c
clustalw2fasta_CFLAGS = $(AM_CFLAGS)
clustalw2fasta_LDADD = libcommon.la
clustalw2fasta_SOURCES = clustalw2fasta.c
clustalw2phylip_CFLAGS = $(AM_CFLAGS)
clustalw2phylip_LDADD = libcommon.la
clustalw2phylip_SOURCES = clustalw2phylip.c
compute_prior_dist_CFLAGS = $(AM_CFLAGS)
compute_prior_dist_LDADD = libcommon.la
compute_prior_dist_SOURCES = compute-prior-dist.c
compute_uniform_priors_CFLAGS = $(AM_CFLAGS)
compute_uniform_priors_LDADD = libcommon.la
compute_uniform_priors_SOURCES = compute-uniform-priors.c
create_priors_CFLAGS = $(AM_CFLAGS)
create_priors_LDADD = libcommon.la -lz
create_priors_SOURCES = create-priors.c
draw_mhmm_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS)
draw_mhmm_LDADD = libcommon.la
draw_mhmm_SOURCES = \
  draw-mhmm.c \
  read-mhmm.c

fasta_get_markov_CFLAGS = $(AM_CFLAGS)
fasta_get_markov_LDADD = libcommon.la
fasta_get_markov_SOURCES = fasta-get-markov.c
fasta_shuffle_letters_CFLAGS = $(AM_CFLAGS)
fasta_shuffle_letters_LDADD = libcommon.la
fasta_shuffle_letters_SOURCES = fasta-shuffle-letters.c ushuffle.c
fasta_io_CFLAGS = -DMAIN $(AM_CFLAGS)
fasta_io_LDADD = libcommon.la
fasta_io_SOURCES = fasta-io.c
fimo_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS)
fimo_LDADD = libcommon.la $(LIBXML2_LIBS)
fimo_SOURCES = fimo.c fimo-output.c
fisher_exact_CFLAGS = -DFE_MAIN $(AM_CFLAGS)
fisher_exact_LDADD = libcommon.la 
fisher_exact_SOURCES = fisher_exact.c
fitevd_CFLAGS = -DMAIN $(AM_CFLAGS)
fitevd_LDADD = libcommon.la
fitevd_SOURCES = fitevd.c
gendb_CFLAGS = -DMAIN $(AM_CFLAGS)
gendb_LDADD = libcommon.la
gendb_SOURCES = gendb.c
getsisze_CFLAGS = $(AM_CFLAGS)
getsize_LDADD = libcommon.la
getsize_SOURCES = getsize.c
glam2_CFLAGS = $(AM_CFLAGS)
glam2_LDADD = libcommon.la
glam2_SOURCES = \
  glam2_alphabet.c \
  glam2_args.c \
  glam2_column_sample.c \
  glam2_dirichlet.c \
  glam2_dna_prior.c \
  glam2_fasta.c \
  glam2_glam2.c \
  glam2_glam2_aln.c \
  glam2_init.c \
  glam2_output.c \
  glam2_recode3_20comp.c \
  glam2_site_sample.c \
  glam2_util.c 

glam2scan_CFLAGS = $(AM_CFLAGS)
glam2scan_LDADD = libcommon.la
glam2scan_SOURCES = \
  glam2_alignment.c \
  glam2_alphabet.c \
  glam2_dna_prior.c \
  glam2_fasta.c \
  glam2_dirichlet.c \
  glam2_heap.c \
  glam2_motif.c \
  glam2_scan.c \
  glam2_scan_args.c \
  glam2_scan_init.c \
  glam2_scan_output.c \
  glam2_recode3_20comp.c \
  glam2_util.c

glam2format_CFLAGS = $(AM_CFLAGS)
glam2format_LDADD = libcommon.la
glam2format_SOURCES = \
  glam2_glam2format.c \
  glam2_alignment.c \
  glam2_fasta.c \
  glam2_util.c

glam2mask_CFLAGS = $(AM_CFLAGS)
glam2mask_LDADD = libcommon.la
glam2mask_SOURCES = \
  glam2_glam2mask.c \
  glam2_alignment.c \
  glam2_fasta.c \
  glam2_util.c 

gomo_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBXSLT_CFLAGS) $(OPENMP_CFLAGS)
gomo_LDADD = libcommon.la $(LIBXML2_LIBS) $(LIBXSLT_LIBS)
gomo_SOURCES = \
  gomo.c \
  gomo_highlight.c \
  merger.c \
  ranksum_test.c \
  read_csv.c

gomo_highlight_CFLAGS = -DMAIN $(AM_CFLAGS)
gomo_highlight_LDADD = libcommon.la
gomo_highlight_SOURCES = gomo_highlight.c
import_html_template_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS)
import_html_template_LDADD = libcommon.la $(LIBXML2_LIBS)
import_html_template_SOURCES = import-html-template.c
mast_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS)
mast_LDADD = libcommon.la $(LIBXML2_LIBS)
mast_SOURCES = \
  diagram.c \
  mast.c

mcast_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS)
mcast_LDADD = libcommon.la $(LIBXML2_LIBS)
mcast_SOURCES = mcast.c
meme2alph_CFLAGS = $(AM_CFLAGS)
meme2alph_LDADD = libcommon.la
meme2alph_SOURCES = meme2alph.c
meme2images_CFLAGS = $(AM_CFLAGS)
meme2images_LDADD = libcommon.la
meme2images_SOURCES = meme2images.c
meme2meme_CFLAGS = $(AM_CFLAGS)
meme2meme_LDADD = libcommon.la
meme2meme_SOURCES = meme2meme.c
meme_get_motif_CFLAGS = $(AM_CFLAGS)
meme_get_motif_LDADD = libcommon.la
meme_get_motif_SOURCES = meme-get-motif.c
mhmm_CFLAGS = -DMAIN $(AM_CFLAGS)
mhmm_LDADD = libcommon.la 
mhmm_SOURCES = mhmm.c
mhmm_io_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS)
mhmm_io_LDADD = libcommon.la 
mhmm_io_SOURCES = mhmm-io.c
mhmme_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS)
mhmme_LDADD = libcommon.la 
mhmme_SOURCES = mhmme.c
mhmms_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS)
mhmms_LDADD = libcommon.la 
mhmms_SOURCES = mhmms.c
mhmmscan_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS)
mhmmscan_LDADD = libcommon.la
mhmmscan_SOURCES = mhmmscan.c
motif_shuffle_columns_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS)
motif_shuffle_columns_LDADD = libcommon.la 
motif_shuffle_columns_SOURCES = motif-shuffle-columns.c
motiph_CFLAGS = -DMOTIPH $(AM_CFLAGS) $(LIBXML2_CFLAGS)
motiph_LDADD = libcommon.la 
motiph_SOURCES = motiph.c
pmp_bf_CFLAGS = -DMOTIPH $(AM_CFLAGS) $(LIBXML2_CFLAGS)
pmp_bf_LDADD = libcommon.la 
pmp_bf_SOURCES = pmp_bf.c
ramen_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS)
ramen_SOURCES = ramen.c ramen_scan.c
ramen_LDADD = libcommon.la $(LIBXML2_LIBS) -lm 
shadow_CFLAGS = -DSHADOW $(AM_CFLAGS) $(LIBXML2_CFLAGS)
shadow_LDADD = libcommon.la 
shadow_SOURCES = shadow.c
llr_CFLAGS = -DMAIN $(AM_CFLAGS)
llr_LDADD = libcommon.la 
llr_SOURCES = llr.c logs.c
spamo_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS)
spamo_LDADD = libcommon.la $(LIBXML2_LIBS)
spamo_SOURCES = \
  cisml-sax.c \
  spamo.c \
  spamo-matches.c \
  spamo-output.c \
  spamo-scan.c

tomtom_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS)
tomtom_LDADD = libcommon.la $(LIBXML2_LIBS)
tomtom_SOURCES = tomtom.c
tree_CFLAGS = -DMAIN $(AM_CFLAGS)
tree_LDADD = libcommon.la 
tree_SOURCES = tree.c
qvalue_CFLAGS = -DMAIN $(AM_CFLAGS)
qvalue_LDADD = libcommon.la -lm
qvalue_SOURCES = qvalue.c
ranksum_test_CFLAGS = -DMAIN $(AM_CFLAGS)
ranksum_test_LDADD = libcommon.la -lm
ranksum_test_SOURCES = ranksum_test.c
reconcile_tree_alignment_CFLAGS = -DMAIN $(AM_CFLAGS)
reconcile_tree_alignment_LDADD = libcommon.la -lm
reconcile_tree_alignment_SOURCES = reconcile-tree-alignment.c
reduce_alignment_CFLAGS = -DMAIN $(AM_CFLAGS)
reduce_alignment_LDADD = libcommon.la -lm
reduce_alignment_SOURCES = reduce-alignment.c
remove_alignment_gaps_CFLAGS = -DMAIN $(AM_CFLAGS)
remove_alignment_gaps_LDADD = libcommon.la -lm
remove_alignment_gaps_SOURCES = remove-alignment-gaps.c
xlate_in_CFLAGS = -DMAIN $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(OPENMP_CFLAGS)
xlate_in_LDADD = libcommon.la $(LIBXML2_LIBS)
xlate_in_SOURCES = xlate-in.c parser-message.c
xsltproc_lite_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS) $(LIBEXSLT_CFLAGS) $(LIBXSLT_CFLAGS)
xsltproc_lite_LDADD = $(LIBXML2_LIBS) $(LIBEXSLT_LIBS) $(LIBXSLT_LIBS) -lm
xsltproc_lite_SOURCES = xsltproc_lite.c
CLEANFILES = dir.h projrel.h $(OBSOLETE_PROGS) $(USELESS_PROGS)
DISTCLEANFILES = dir.h projrel.h $(OBSOLETE_PROGS) $(USELESS_PROGS)

#all the header files
EXTRA_DIST = \
  aa.h \
  align.h \
  alignment.h \
	alph-in.h \
  alphabet.h \
  ame.h \
  array.h \
  array-list.h \
  banner.h \
  beadstring.h \
  beadstring-xml.h \
  binary-search.h \
  binomial.h \
  buffer.h \
  build-hmm.h \
  calculate_p_y.h \
  ceqlogo.h \
  cisml-dtd.h \
  cisml.h \
  cisml-sax.h \
  clustalw-io.h \
  curves.h \
  diagram.h \
  display_globals.h \
  display.h \
  dpalign.h \
  dp.h \
  dreme-sax.h \
  eps2png.h \
  em.h \
  empirical-qvalue.h \
  evomodel.h \
  fasta-io.h \
  fimo.h \
  fimo-html-string.h \
  fimo-output.h \
  fisher_exact.h \
  fitevd.h \
  gendb.h \
  general.h \
  glam2_alignment.h \
  glam2_alphabet.h \
  glam2_args.h \
  glam2_column_sample.h \
  glam2_convolve.h \
  glam2_dirichlet.h \
  glam2_dna_prior.h \
  glam2_fasta.h \
  glam2_glam2_aln.h \
  glam2_glam2.h \
  glam2_heap.h \
  glam2_init.h \
  glam2_motif.h \
  glam2_output.h \
  glam2_recode3_20comp.h \
  glam2_scan_args.h \
  glam2_scan.h \
  glam2_scan_init.h \
  glam2_scan_output.h \
  glam2_site_sample.h \
  glam2_util.h \
  glam2_version.h \
  gomo_highlight.h \
  hash.h \
  hash_table.h \
  hash_table_string.h \
  heap.h \
  histogram.h \
  html-data.h \
  html-monolith.h \
  ic.h \
  io.h \
  json-checker.h \
  json-reader.h \
  json-writer.h \
  karlin.h \
  linked-list.h \
  llr.h \
  log-hmm.h \
  logodds.h \
  logs.h \
  macros.h \
  mast.h \
  match.h \
  matrix.h \
  mcast-match.h \
  meme-dtd.h \
  meme.h \
  meme-sax.h \
  merger.h \
  message.h \
  metameme.h \
  meta-pssm-distr.h \
  mhmm-dtd.h \
  mhmm.h \
  mhmms.h \
  mhmmscan.h \
  mhmm-state.h \
  momo.h \
  momo-algorithm.h \
  momo-html-string.h \
  momo-input.h \
	momo-modl.h \
	momo-motifx.h \
  momo-output.h \
	momo-simple.h \
  motif.h \
  motif-in.h \
  motif-in-common.h \
  motif-in-dreme-xml.h \
  motif-in-flags.h \
  motif-in-meme-html.h \
  motif-in-meme-json.h \
  motif-in-meme-text.h \
  motif-in-meme-xml.h \
  motif-spec.h \
  motif_regexp.h \
  motifs.h \
  motiph-scoring.h \
  mp.h \
  mtwist.h \
  mtype.h \
  nrutil.h \
  object-list.h \
  order.h \
  params.h \
	parser-message.h \
  partition.h \
  prior.h \
  prior-dist.h \
  data-block.h \
  data-block-reader.h \
	parser-message.h \
  prealigned-io.h \
  prior-reader-from-psp.h \
  prior-reader-from-wig.h \
  psp.h \
  pssm-distr.h \
  pssm.h \
  qvalue.h \
  ramen_scan.h \
  ranksum_test.h \
  reservoir.h \
  rdb-matrix.h \
  read_csv.h \
  read-mhmm.h \
  read_seq_file.h \
  read_sequence.h \
  red-black-tree.h \
  regex-utils.h \
  regress.h \
  sax-parser-utils.h \
  scanned-sequence.h \
  scored-sites.h \
  seed_diffs.h \
  seed.h \
  seq.h \
  seq-reader-from-fasta.h \
  shuffle_int.h \
  simple-getopt.h \
  spamo-cisml.h \
  spamo-matches.h \
  spamo-output.h \
  spamo-scan.h \
  split.h \
  sp_matrix.h \
  star.h \
  string-builder.h \
  string-list.h \
  string-match.h \
  strlcpy.h \
  subst-matrix.h \
  substmatrix-table.h \
  transfac.h \
  tree.h \
  user.h \
  ushuffle.h \
  utest.h \
  utils.h \
  wiggle-reader.h \
  write-mhmm.h \
	xlate-in.h \
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  xml-util.h \
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libcommon_la-alignment.lo: alignment.c
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libcommon_la-alph-in.lo: alph-in.c
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libcommon_la-alphabet.lo: alphabet.c
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libcommon_la-array.lo: array.c
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libcommon_la-array-list.lo: array-list.c
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libcommon_la-binary-search.lo: binary-search.c
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libcommon_la-binomial.lo: binomial.c
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libcommon_la-build-hmm.lo: build-hmm.c
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libcommon_la-buffer.lo: buffer.c
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libcommon_la-ceqlogo.lo: ceqlogo.c
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libcommon_la-cisml.lo: cisml.c
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libcommon_la-cisml-sax.lo: cisml-sax.c
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libcommon_la-clustalw-io.lo: clustalw-io.c
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libcommon_la-dp.lo: dp.c
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libcommon_la-dreme-sax.lo: dreme-sax.c
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libcommon_la-eps2png.lo: eps2png.c
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libcommon_la-empirical-qvalue.lo: empirical-qvalue.c
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libcommon_la-evomodel.lo: evomodel.c
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libcommon_la-fasta-io.lo: fasta-io.c
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libcommon_la-fitevd.lo: fitevd.c
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libcommon_la-gendb.lo: gendb.c
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libcommon_la-hash_table.lo: hash_table.c
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libcommon_la-heap.lo: heap.c
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libcommon_la-html-data.lo: html-data.c
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libcommon_la-html-monolith.lo: html-monolith.c
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libcommon_la-io.lo: io.c
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libcommon_la-json-checker.lo: json-checker.c
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libcommon_la-json-reader.lo: json-reader.c
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libcommon_la-json-writer.lo: json-writer.c
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libcommon_la-karlin.lo: karlin.c
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libcommon_la-linked-list.lo: linked-list.c
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libcommon_la-log-hmm.lo: log-hmm.c
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libcommon_la-logodds.lo: logodds.c
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libcommon_la-mast-util.lo: mast-util.c
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libcommon_la-motif-in.lo: motif-in.c
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libcommon_la-motif.lo: motif.c
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libcommon_la-motif_regexp.lo: motif_regexp.c
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libcommon_la-motifs.lo: motifs.c
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libcommon_la-motiph-scoring.lo: motiph-scoring.c
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libcommon_la-mtwist.lo: mtwist.c
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libcommon_la-object-list.lo: object-list.c
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libcommon_la-order.lo: order.c
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libcommon_la-data-block.lo: data-block.c
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libcommon_la-data-block-reader.lo: data-block-reader.c
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libcommon_la-parser-message.lo: parser-message.c
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libcommon_la-prealigned-io.lo: prealigned-io.c
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libcommon_la-prior-reader-from-psp.lo: prior-reader-from-psp.c
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libcommon_la-prior-reader-from-wig.lo: prior-reader-from-wig.c
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libcommon_la-prior-dist.lo: prior-dist.c
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libcommon_la-pssm.lo: pssm.c
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libcommon_la-pssm-distr.lo: pssm-distr.c
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libcommon_la-qvalue.lo: qvalue.c
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libcommon_la-ranksum_test.lo: ranksum_test.c
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libcommon_la-rdb-matrix.lo: rdb-matrix.c
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libcommon_la-read-mhmm.lo: read-mhmm.c
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libcommon_la-read_sequence.lo: read_sequence.c
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libcommon_la-red-black-tree.lo: red-black-tree.c
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libcommon_la-regex-utils.lo: regex-utils.c
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libcommon_la-regress.lo: regress.c
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libcommon_la-reservoir.lo: reservoir.c
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libcommon_la-sax-parser-utils.lo: sax-parser-utils.c
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libcommon_la-scanned-sequence.lo: scanned-sequence.c
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libcommon_la-scored-sites.lo: scored-sites.c
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libcommon_la-seq.lo: seq.c
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libcommon_la-seq-reader-from-fasta.lo: seq-reader-from-fasta.c
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libcommon_la-simple-getopt.lo: simple-getopt.c
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libcommon_la-spearman-rank-correlation.lo: spearman-rank-correlation.c
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libcommon_la-string-builder.lo: string-builder.c
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libcommon_la-string-list.lo: string-list.c
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libcommon_la-string-match.lo: string-match.c
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libcommon_la-subst-matrix.lo: subst-matrix.c
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libcommon_la-substmatrix-table.lo: substmatrix-table.c
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libcommon_la-transfac.lo: transfac.c
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libcommon_la-tree.lo: tree.c
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libcommon_la-utils.lo: utils.c
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libcommon_la-wiggle-reader.lo: wiggle-reader.c
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libcommon_la-write-mhmm.lo: write-mhmm.c
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libcommon_la-xlate-in.lo: xlate-in.c
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libcommon_la-xml-out.lo: xml-out.c
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libcommon_la-xml-util.lo: xml-util.c
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alph_in-alph-in.o: alph-in.c
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alph_in-alph-in.obj: alph-in.c
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alph_in-parser-message.o: parser-message.c
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alphtype-alphtype.o: alphtype.c
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glam2-glam2_glam2.o: glam2_glam2.c
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glam2-glam2_glam2_aln.o: glam2_glam2_aln.c
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glam2mask-glam2_alignment.o: glam2_alignment.c
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glam2mask-glam2_alignment.obj: glam2_alignment.c
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glam2mask-glam2_fasta.o: glam2_fasta.c
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glam2mask-glam2_fasta.obj: glam2_fasta.c
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glam2mask-glam2_util.o: glam2_util.c
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glam2mask-glam2_util.obj: glam2_util.c
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glam2scan-glam2_alignment.o: glam2_alignment.c
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glam2scan-glam2_alignment.obj: glam2_alignment.c
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glam2scan-glam2_alphabet.o: glam2_alphabet.c
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glam2scan-glam2_alphabet.obj: glam2_alphabet.c
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glam2scan-glam2_dna_prior.o: glam2_dna_prior.c
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glam2scan-glam2_dna_prior.obj: glam2_dna_prior.c
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glam2scan-glam2_fasta.o: glam2_fasta.c
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glam2scan-glam2_fasta.obj: glam2_fasta.c
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glam2scan-glam2_dirichlet.o: glam2_dirichlet.c
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glam2scan-glam2_dirichlet.obj: glam2_dirichlet.c
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glam2scan-glam2_heap.o: glam2_heap.c
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glam2scan-glam2_heap.obj: glam2_heap.c
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glam2scan-glam2_motif.o: glam2_motif.c
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glam2scan-glam2_motif.obj: glam2_motif.c
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glam2scan-glam2_scan.o: glam2_scan.c
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glam2scan-glam2_scan.obj: glam2_scan.c
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glam2scan-glam2_scan_args.o: glam2_scan_args.c
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glam2scan-glam2_scan_args.obj: glam2_scan_args.c
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glam2scan-glam2_scan_init.o: glam2_scan_init.c
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glam2scan-glam2_scan_init.obj: glam2_scan_init.c
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glam2scan-glam2_scan_output.o: glam2_scan_output.c
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glam2scan-glam2_scan_output.obj: glam2_scan_output.c
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glam2scan-glam2_recode3_20comp.o: glam2_recode3_20comp.c
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glam2scan-glam2_recode3_20comp.obj: glam2_recode3_20comp.c
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glam2scan-glam2_util.o: glam2_util.c
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glam2scan-glam2_util.obj: glam2_util.c
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gomo-gomo.o: gomo.c
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	echo '#define TEMP_DIR "$(MEME_TEMP)" ' >> $@

projrel.h: ../ARCHIVE_REVISION ../ARCHIVE_DATE
	echo '#define REVISION "$(ARCHIVE_REVISION)"' > $@
	echo '#define ARCHIVE_DATE "$(ARCHIVE_DATE)"' >> $@
  #spamo-cisml.c

# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT: