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  dtc \
  fasta-get-markov \
  fasta-shuffle-letters \
  fasta-from-bed \
  fisher_exact \
  fitevd \
  gendb \
  getsize \
  glam2format \
  glam2mask \
  gomo_highlight \
  import-html-template \
  index-fasta-file \
  llr \
  meme2alph \
  meme2images \
  meme2meme \
  meme-get-motif \
  motif-shuffle-columns \
  motiph \
  pmp_bf \
  ramen \
  qvalue \
  ranksum_test \
  reconcile-tree-alignment \
  reduce-alignment \
  remove-alignment-gaps

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) \
        -DSTREEHUGE

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

libcommon_la_SOURCES = \
  alignment.c \
  alph-in.c \
  alphabet.c \
  array.c \
  array-list.c \
  bates.c \
  bed.c \
  bed-io.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 \
  fasta-get-markov.c \
  fitevd.c \
  gendb.c \
  gtf.c \
  gtf-io.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 \
  log_erfc.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 \
  momo-algorithm.c \
  momo-input.c \
  momo-modl.c \
  momo-motifx.c \
  momo-output.c \
  momo-simple.c \
  motif.c \
  motif-db.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-in-streme-xml.c \
  motif_regexp.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 \
  random-variate.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 \
  streme-sax.c \
  streme-utils.c \
  string-builder.c \
  string-list.c \
  string-match.c \
  subst-matrix.c \
  substmatrix-table.c \
  transfac.c \
  tree.c \
  utils.c \
  ushuffle.c \
  wiggle-reader.c \
  write-mhmm.c \
  xlate-in.c \
  xml-out.c \
  xml-util.c \
  inputmultiseq.c \
  st_access.c \
  st_construct.c \
  st_dfs.c \
  st_mapfile.c \
  st_seterror.c \
  st_space.c \
  banner.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_LDADD = libcommon.la $(LIBXML2_LIBS) -lm 
ame_SOURCES = ame.c ramen_scan.c fisher_exact.c
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
tgene_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS)
tgene_LDADD = libcommon.la $(LIBXML2_LIBS)
tgene_SOURCES = tgene.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_from_bed_CFLAGS = -DMAIN $(AM_CFLAGS)
fasta_from_bed_LDADD = libcommon.la
fasta_from_bed_SOURCES = fasta-from-bed.c
fasta_get_markov_CFLAGS = -DMAIN $(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
index_fasta_file_CFLAGS = $(AM_CFLAGS) 
index_fasta_file_LDADD = libcommon.la
index_fasta_file_SOURCES = index-fasta-file.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
momo_CFLAGS = $(AM_CFLAGS) $(LIBXML2_CFLAGS)
momo_LDADD = libcommon.la $(LIBXML2_LIBS)
momo_SOURCES = momo.c fisher_exact.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
streme_CFLAGS = -DSTREEHUGE $(AM_CFLAGS) $(LIBXML2_CFLAGS)
streme_LDADD = libcommon.la $(LIBXML2_LIBS)
streme_SOURCES = streme.c fisher_exact.c 
enr_CFLAGS = -DSTREEHUGE $(AM_CFLAGS) $(LIBXML2_CFLAGS)
enr_LDADD = libcommon.la $(LIBXML2_LIBS)
enr_SOURCES = enr.c fisher_exact.c 
llr_CFLAGS = -DMAIN $(AM_CFLAGS)
llr_LDADD = libcommon.la 
llr_SOURCES = llr.c logs.c
dtc_CFLAGS = -DMAIN $(AM_CFLAGS)
dtc_LDADD = libcommon.la 
dtc_SOURCES = dtc.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
CLEANFILES = dir.h projrel.h \
	dreme dreme-py3 fasta-dinucleotide-shuffle fasta-hamming-enrich \
	glam2html glam2psfm glam2scan2html meme  \
	$(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 \
  bates.h \
  beadstring.h \
  beadstring-xml.h \
  bed.h \
  bed-io.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 \
  data_types.h \
  diagram.h \
  display.h \
  dpalign.h \
  dp.h \
  dtc.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 \
  gtf.h \
  gtf-io.h \
  hash_table.h \
  hash_table_string.h \
  heap.h \
  histogram.h \
  html-data.h \
  html-monolith.h \
  ic.h \
  inputmultiseq.h \
  io.h \
  json-checker.h \
  json-reader.h \
  json-writer.h \
  karlin.h \
  linked-list.h \
  llr.h \
  log-hmm.h \
  log_erfc.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-input.h \
  momo-modl.h \
  momo-motifx.h \
  momo-output.h \
  momo-simple.h \
  motif.h \
  motif-db.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-in-streme-xml.h \
  motif-spec.h \
  motif_regexp.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 \
  prealigned-io.h \
  prior-reader-from-psp.h \
  prior-reader-from-wig.h \
  psp.h \
  pssm-distr.h \
  pssm.h \
  qvalue.h \
  random-variate.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 \
  spearman-rank-correlation.h \
  split.h \
  sp_matrix.h \
  spearman-rank-correlation.h \
  star.h \
  streme-sax.h \
  streme-utils.h \
  string-builder.h \
  string-list.h \
  string-match.h \
  strlcpy.h \
  st_arraydef.h \
  st_construct_gen.h \
  st_debugdef.h \
  st_dfs_gen.h \
  st_errordef.h \
  st_intbits.h \
  st_megabytes.h \
  st_multidef.h \
  st_spacedef.h \
  st_streeacc.h \
  st_streehuge.h \
  st_streemac.h \
  st_streetyp.h \
  st_symboldef.h \
  st_types.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 \
  xml-out.h \
  xml-util.h \
  zscore.h

all: $(BUILT_SOURCES)
	$(MAKE) $(AM_MAKEFLAGS) all-recursive

.SUFFIXES:
.SUFFIXES: .c .lo .o .obj
$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
	@for dep in $?; do \
	  case '$(am__configure_deps)' in \
	    *$$dep*) \
	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
	        && { if test -f $@; then exit 0; else break; fi; }; \
	      exit 1;; \
	  esac; \
	done; \
	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
	$(am__cd) $(top_srcdir) && \
	  $(AUTOMAKE) --gnu src/Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
	@case '$?' in \
	  *config.status*) \
	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
	  *) \
	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
	esac;

$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh

$(top_srcdir)/configure:  $(am__configure_deps)
	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(am__aclocal_m4_deps):
install-binPROGRAMS: $(bin_PROGRAMS)
	@$(NORMAL_INSTALL)
	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
	if test -n "$$list"; then \
	  echo " $(MKDIR_P) '$(DESTDIR)$(bindir)'"; \
	  $(MKDIR_P) "$(DESTDIR)$(bindir)" || exit 1; \
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	for p in $$list; do echo "$$p $$p"; done | \
	sed 's/$(EXEEXT)$$//' | \
	while read p p1; do if test -f $$p \
	 || test -f $$p1 \
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	done | \
	sed -e 'p;s,.*/,,;n;h' \
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	sed 'N;N;N;s,\n, ,g' | \
	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
	  { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
	    if ($$2 == $$4) files[d] = files[d] " " $$1; \
	    else { print "f", $$3 "/" $$4, $$1; } } \
	  END { for (d in files) print "f", d, files[d] }' | \
	while read type dir files; do \
	    if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
	    test -z "$$files" || { \
	    echo " $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
	    $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
	    } \
	; done

uninstall-binPROGRAMS:
	@$(NORMAL_UNINSTALL)
	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
	files=`for p in $$list; do echo "$$p"; done | \
	  sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
	      -e 's/$$/$(EXEEXT)/' \
	`; \
	test -n "$$list" || exit 0; \
	echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
	cd "$(DESTDIR)$(bindir)" && rm -f $$files

clean-binPROGRAMS:
	@list='$(bin_PROGRAMS)'; test -n "$$list" || exit 0; \
	echo " rm -f" $$list; \
	rm -f $$list || exit $$?; \
	test -n "$(EXEEXT)" || exit 0; \
	list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
	echo " rm -f" $$list; \
	rm -f $$list
install-memelibexecPROGRAMS: $(memelibexec_PROGRAMS)
	@$(NORMAL_INSTALL)
	@list='$(memelibexec_PROGRAMS)'; test -n "$(memelibexecdir)" || list=; \
	if test -n "$$list"; then \
	  echo " $(MKDIR_P) '$(DESTDIR)$(memelibexecdir)'"; \
	  $(MKDIR_P) "$(DESTDIR)$(memelibexecdir)" || exit 1; \
	fi; \
	for p in $$list; do echo "$$p $$p"; done | \
	sed 's/$(EXEEXT)$$//' | \
	while read p p1; do if test -f $$p \
	 || test -f $$p1 \
	  ; then echo "$$p"; echo "$$p"; else :; fi; \
	done | \
	sed -e 'p;s,.*/,,;n;h' \
	    -e 's|.*|.|' \
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	sed 'N;N;N;s,\n, ,g' | \
	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
	  { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
	    if ($$2 == $$4) files[d] = files[d] " " $$1; \
	    else { print "f", $$3 "/" $$4, $$1; } } \
	  END { for (d in files) print "f", d, files[d] }' | \
	while read type dir files; do \
	    if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
	    test -z "$$files" || { \
	    echo " $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(memelibexecdir)$$dir'"; \
	    $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(memelibexecdir)$$dir" || exit $$?; \
	    } \
	; done

uninstall-memelibexecPROGRAMS:
	@$(NORMAL_UNINSTALL)
	@list='$(memelibexec_PROGRAMS)'; test -n "$(memelibexecdir)" || list=; \
	files=`for p in $$list; do echo "$$p"; done | \
	  sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
	      -e 's/$$/$(EXEEXT)/' \
	`; \
	test -n "$$list" || exit 0; \
	echo " ( cd '$(DESTDIR)$(memelibexecdir)' && rm -f" $$files ")"; \
	cd "$(DESTDIR)$(memelibexecdir)" && rm -f $$files

clean-memelibexecPROGRAMS:
	@list='$(memelibexec_PROGRAMS)'; test -n "$$list" || exit 0; \
	echo " rm -f" $$list; \
	rm -f $$list || exit $$?; \
	test -n "$(EXEEXT)" || exit 0; \
	list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
	echo " rm -f" $$list; \
	rm -f $$list

clean-noinstLTLIBRARIES:
	-test -z "$(noinst_LTLIBRARIES)" || rm -f $(noinst_LTLIBRARIES)
	@list='$(noinst_LTLIBRARIES)'; \
	locs=`for p in $$list; do echo $$p; done | \
	      sed 's|^[^/]*$$|.|; s|/[^/]*$$||; s|$$|/so_locations|' | \
	      sort -u`; \
	test -z "$$locs" || { \
	  echo rm -f $${locs}; \
	  rm -f $${locs}; \
	}

libcommon.la: $(libcommon_la_OBJECTS) $(libcommon_la_DEPENDENCIES) $(EXTRA_libcommon_la_DEPENDENCIES) 
	$(AM_V_CCLD)$(libcommon_la_LINK)  $(libcommon_la_OBJECTS) $(libcommon_la_LIBADD) $(LIBS)

alph-in$(EXEEXT): $(alph_in_OBJECTS) $(alph_in_DEPENDENCIES) $(EXTRA_alph_in_DEPENDENCIES) 
	@rm -f alph-in$(EXEEXT)
	$(AM_V_CCLD)$(alph_in_LINK) $(alph_in_OBJECTS) $(alph_in_LDADD) $(LIBS)

alphtype$(EXEEXT): $(alphtype_OBJECTS) $(alphtype_DEPENDENCIES) $(EXTRA_alphtype_DEPENDENCIES) 
	@rm -f alphtype$(EXEEXT)
	$(AM_V_CCLD)$(alphtype_LINK) $(alphtype_OBJECTS) $(alphtype_LDADD) $(LIBS)

ama$(EXEEXT): $(ama_OBJECTS) $(ama_DEPENDENCIES) $(EXTRA_ama_DEPENDENCIES) 
	@rm -f ama$(EXEEXT)
	$(AM_V_CCLD)$(ama_LINK) $(ama_OBJECTS) $(ama_LDADD) $(LIBS)

ame$(EXEEXT): $(ame_OBJECTS) $(ame_DEPENDENCIES) $(EXTRA_ame_DEPENDENCIES) 
	@rm -f ame$(EXEEXT)
	$(AM_V_CCLD)$(ame_LINK) $(ame_OBJECTS) $(ame_LDADD) $(LIBS)

beadstring$(EXEEXT): $(beadstring_OBJECTS) $(beadstring_DEPENDENCIES) $(EXTRA_beadstring_DEPENDENCIES) 
	@rm -f beadstring$(EXEEXT)
	$(AM_V_CCLD)$(beadstring_LINK) $(beadstring_OBJECTS) $(beadstring_LDADD) $(LIBS)

centrimo$(EXEEXT): $(centrimo_OBJECTS) $(centrimo_DEPENDENCIES) $(EXTRA_centrimo_DEPENDENCIES) 
	@rm -f centrimo$(EXEEXT)
	$(AM_V_CCLD)$(centrimo_LINK) $(centrimo_OBJECTS) $(centrimo_LDADD) $(LIBS)

ceqlogo$(EXEEXT): $(ceqlogo_OBJECTS) $(ceqlogo_DEPENDENCIES) $(EXTRA_ceqlogo_DEPENDENCIES) 
	@rm -f ceqlogo$(EXEEXT)
	$(AM_V_CCLD)$(ceqlogo_LINK) $(ceqlogo_OBJECTS) $(ceqlogo_LDADD) $(LIBS)

clustalw-io$(EXEEXT): $(clustalw_io_OBJECTS) $(clustalw_io_DEPENDENCIES) $(EXTRA_clustalw_io_DEPENDENCIES) 
	@rm -f clustalw-io$(EXEEXT)
	$(AM_V_CCLD)$(clustalw_io_LINK) $(clustalw_io_OBJECTS) $(clustalw_io_LDADD) $(LIBS)

clustalw2fasta$(EXEEXT): $(clustalw2fasta_OBJECTS) $(clustalw2fasta_DEPENDENCIES) $(EXTRA_clustalw2fasta_DEPENDENCIES) 
	@rm -f clustalw2fasta$(EXEEXT)
	$(AM_V_CCLD)$(clustalw2fasta_LINK) $(clustalw2fasta_OBJECTS) $(clustalw2fasta_LDADD) $(LIBS)

clustalw2phylip$(EXEEXT): $(clustalw2phylip_OBJECTS) $(clustalw2phylip_DEPENDENCIES) $(EXTRA_clustalw2phylip_DEPENDENCIES) 
	@rm -f clustalw2phylip$(EXEEXT)
	$(AM_V_CCLD)$(clustalw2phylip_LINK) $(clustalw2phylip_OBJECTS) $(clustalw2phylip_LDADD) $(LIBS)

compute-prior-dist$(EXEEXT): $(compute_prior_dist_OBJECTS) $(compute_prior_dist_DEPENDENCIES) $(EXTRA_compute_prior_dist_DEPENDENCIES) 
	@rm -f compute-prior-dist$(EXEEXT)
	$(AM_V_CCLD)$(compute_prior_dist_LINK) $(compute_prior_dist_OBJECTS) $(compute_prior_dist_LDADD) $(LIBS)

compute-uniform-priors$(EXEEXT): $(compute_uniform_priors_OBJECTS) $(compute_uniform_priors_DEPENDENCIES) $(EXTRA_compute_uniform_priors_DEPENDENCIES) 
	@rm -f compute-uniform-priors$(EXEEXT)
	$(AM_V_CCLD)$(compute_uniform_priors_LINK) $(compute_uniform_priors_OBJECTS) $(compute_uniform_priors_LDADD) $(LIBS)

create-priors$(EXEEXT): $(create_priors_OBJECTS) $(create_priors_DEPENDENCIES) $(EXTRA_create_priors_DEPENDENCIES) 
	@rm -f create-priors$(EXEEXT)
	$(AM_V_CCLD)$(create_priors_LINK) $(create_priors_OBJECTS) $(create_priors_LDADD) $(LIBS)

draw-mhmm$(EXEEXT): $(draw_mhmm_OBJECTS) $(draw_mhmm_DEPENDENCIES) $(EXTRA_draw_mhmm_DEPENDENCIES) 
	@rm -f draw-mhmm$(EXEEXT)
	$(AM_V_CCLD)$(draw_mhmm_LINK) $(draw_mhmm_OBJECTS) $(draw_mhmm_LDADD) $(LIBS)

dtc$(EXEEXT): $(dtc_OBJECTS) $(dtc_DEPENDENCIES) $(EXTRA_dtc_DEPENDENCIES) 
	@rm -f dtc$(EXEEXT)
	$(AM_V_CCLD)$(dtc_LINK) $(dtc_OBJECTS) $(dtc_LDADD) $(LIBS)

enr$(EXEEXT): $(enr_OBJECTS) $(enr_DEPENDENCIES) $(EXTRA_enr_DEPENDENCIES) 
	@rm -f enr$(EXEEXT)
	$(AM_V_CCLD)$(enr_LINK) $(enr_OBJECTS) $(enr_LDADD) $(LIBS)

fasta-from-bed$(EXEEXT): $(fasta_from_bed_OBJECTS) $(fasta_from_bed_DEPENDENCIES) $(EXTRA_fasta_from_bed_DEPENDENCIES) 
	@rm -f fasta-from-bed$(EXEEXT)
	$(AM_V_CCLD)$(fasta_from_bed_LINK) $(fasta_from_bed_OBJECTS) $(fasta_from_bed_LDADD) $(LIBS)

fasta-get-markov$(EXEEXT): $(fasta_get_markov_OBJECTS) $(fasta_get_markov_DEPENDENCIES) $(EXTRA_fasta_get_markov_DEPENDENCIES) 
	@rm -f fasta-get-markov$(EXEEXT)
	$(AM_V_CCLD)$(fasta_get_markov_LINK) $(fasta_get_markov_OBJECTS) $(fasta_get_markov_LDADD) $(LIBS)

fasta-io$(EXEEXT): $(fasta_io_OBJECTS) $(fasta_io_DEPENDENCIES) $(EXTRA_fasta_io_DEPENDENCIES) 
	@rm -f fasta-io$(EXEEXT)
	$(AM_V_CCLD)$(fasta_io_LINK) $(fasta_io_OBJECTS) $(fasta_io_LDADD) $(LIBS)

fasta-shuffle-letters$(EXEEXT): $(fasta_shuffle_letters_OBJECTS) $(fasta_shuffle_letters_DEPENDENCIES) $(EXTRA_fasta_shuffle_letters_DEPENDENCIES) 
	@rm -f fasta-shuffle-letters$(EXEEXT)
	$(AM_V_CCLD)$(fasta_shuffle_letters_LINK) $(fasta_shuffle_letters_OBJECTS) $(fasta_shuffle_letters_LDADD) $(LIBS)

fimo$(EXEEXT): $(fimo_OBJECTS) $(fimo_DEPENDENCIES) $(EXTRA_fimo_DEPENDENCIES) 
	@rm -f fimo$(EXEEXT)
	$(AM_V_CCLD)$(fimo_LINK) $(fimo_OBJECTS) $(fimo_LDADD) $(LIBS)

fisher_exact$(EXEEXT): $(fisher_exact_OBJECTS) $(fisher_exact_DEPENDENCIES) $(EXTRA_fisher_exact_DEPENDENCIES) 
	@rm -f fisher_exact$(EXEEXT)
	$(AM_V_CCLD)$(fisher_exact_LINK) $(fisher_exact_OBJECTS) $(fisher_exact_LDADD) $(LIBS)

fitevd$(EXEEXT): $(fitevd_OBJECTS) $(fitevd_DEPENDENCIES) $(EXTRA_fitevd_DEPENDENCIES) 
	@rm -f fitevd$(EXEEXT)
	$(AM_V_CCLD)$(fitevd_LINK) $(fitevd_OBJECTS) $(fitevd_LDADD) $(LIBS)

gendb$(EXEEXT): $(gendb_OBJECTS) $(gendb_DEPENDENCIES) $(EXTRA_gendb_DEPENDENCIES) 
	@rm -f gendb$(EXEEXT)
	$(AM_V_CCLD)$(gendb_LINK) $(gendb_OBJECTS) $(gendb_LDADD) $(LIBS)

getsize$(EXEEXT): $(getsize_OBJECTS) $(getsize_DEPENDENCIES) $(EXTRA_getsize_DEPENDENCIES) 
	@rm -f getsize$(EXEEXT)
	$(AM_V_CCLD)$(LINK) $(getsize_OBJECTS) $(getsize_LDADD) $(LIBS)

glam2$(EXEEXT): $(glam2_OBJECTS) $(glam2_DEPENDENCIES) $(EXTRA_glam2_DEPENDENCIES) 
	@rm -f glam2$(EXEEXT)
	$(AM_V_CCLD)$(glam2_LINK) $(glam2_OBJECTS) $(glam2_LDADD) $(LIBS)

glam2format$(EXEEXT): $(glam2format_OBJECTS) $(glam2format_DEPENDENCIES) $(EXTRA_glam2format_DEPENDENCIES) 
	@rm -f glam2format$(EXEEXT)
	$(AM_V_CCLD)$(glam2format_LINK) $(glam2format_OBJECTS) $(glam2format_LDADD) $(LIBS)

glam2mask$(EXEEXT): $(glam2mask_OBJECTS) $(glam2mask_DEPENDENCIES) $(EXTRA_glam2mask_DEPENDENCIES) 
	@rm -f glam2mask$(EXEEXT)
	$(AM_V_CCLD)$(glam2mask_LINK) $(glam2mask_OBJECTS) $(glam2mask_LDADD) $(LIBS)

glam2scan$(EXEEXT): $(glam2scan_OBJECTS) $(glam2scan_DEPENDENCIES) $(EXTRA_glam2scan_DEPENDENCIES) 
	@rm -f glam2scan$(EXEEXT)
	$(AM_V_CCLD)$(glam2scan_LINK) $(glam2scan_OBJECTS) $(glam2scan_LDADD) $(LIBS)

gomo$(EXEEXT): $(gomo_OBJECTS) $(gomo_DEPENDENCIES) $(EXTRA_gomo_DEPENDENCIES) 
	@rm -f gomo$(EXEEXT)
	$(AM_V_CCLD)$(gomo_LINK) $(gomo_OBJECTS) $(gomo_LDADD) $(LIBS)

gomo_highlight$(EXEEXT): $(gomo_highlight_OBJECTS) $(gomo_highlight_DEPENDENCIES) $(EXTRA_gomo_highlight_DEPENDENCIES) 
	@rm -f gomo_highlight$(EXEEXT)
	$(AM_V_CCLD)$(gomo_highlight_LINK) $(gomo_highlight_OBJECTS) $(gomo_highlight_LDADD) $(LIBS)

import-html-template$(EXEEXT): $(import_html_template_OBJECTS) $(import_html_template_DEPENDENCIES) $(EXTRA_import_html_template_DEPENDENCIES) 
	@rm -f import-html-template$(EXEEXT)
	$(AM_V_CCLD)$(import_html_template_LINK) $(import_html_template_OBJECTS) $(import_html_template_LDADD) $(LIBS)

index-fasta-file$(EXEEXT): $(index_fasta_file_OBJECTS) $(index_fasta_file_DEPENDENCIES) $(EXTRA_index_fasta_file_DEPENDENCIES) 
	@rm -f index-fasta-file$(EXEEXT)
	$(AM_V_CCLD)$(index_fasta_file_LINK) $(index_fasta_file_OBJECTS) $(index_fasta_file_LDADD) $(LIBS)

llr$(EXEEXT): $(llr_OBJECTS) $(llr_DEPENDENCIES) $(EXTRA_llr_DEPENDENCIES) 
	@rm -f llr$(EXEEXT)
	$(AM_V_CCLD)$(llr_LINK) $(llr_OBJECTS) $(llr_LDADD) $(LIBS)

mast$(EXEEXT): $(mast_OBJECTS) $(mast_DEPENDENCIES) $(EXTRA_mast_DEPENDENCIES) 
	@rm -f mast$(EXEEXT)
	$(AM_V_CCLD)$(mast_LINK) $(mast_OBJECTS) $(mast_LDADD) $(LIBS)

mcast$(EXEEXT): $(mcast_OBJECTS) $(mcast_DEPENDENCIES) $(EXTRA_mcast_DEPENDENCIES) 
	@rm -f mcast$(EXEEXT)
	$(AM_V_CCLD)$(mcast_LINK) $(mcast_OBJECTS) $(mcast_LDADD) $(LIBS)

meme-get-motif$(EXEEXT): $(meme_get_motif_OBJECTS) $(meme_get_motif_DEPENDENCIES) $(EXTRA_meme_get_motif_DEPENDENCIES) 
	@rm -f meme-get-motif$(EXEEXT)
	$(AM_V_CCLD)$(meme_get_motif_LINK) $(meme_get_motif_OBJECTS) $(meme_get_motif_LDADD) $(LIBS)

meme2alph$(EXEEXT): $(meme2alph_OBJECTS) $(meme2alph_DEPENDENCIES) $(EXTRA_meme2alph_DEPENDENCIES) 
	@rm -f meme2alph$(EXEEXT)
	$(AM_V_CCLD)$(meme2alph_LINK) $(meme2alph_OBJECTS) $(meme2alph_LDADD) $(LIBS)

meme2images$(EXEEXT): $(meme2images_OBJECTS) $(meme2images_DEPENDENCIES) $(EXTRA_meme2images_DEPENDENCIES) 
	@rm -f meme2images$(EXEEXT)
	$(AM_V_CCLD)$(meme2images_LINK) $(meme2images_OBJECTS) $(meme2images_LDADD) $(LIBS)

meme2meme$(EXEEXT): $(meme2meme_OBJECTS) $(meme2meme_DEPENDENCIES) $(EXTRA_meme2meme_DEPENDENCIES) 
	@rm -f meme2meme$(EXEEXT)
	$(AM_V_CCLD)$(meme2meme_LINK) $(meme2meme_OBJECTS) $(meme2meme_LDADD) $(LIBS)

mhmm$(EXEEXT): $(mhmm_OBJECTS) $(mhmm_DEPENDENCIES) $(EXTRA_mhmm_DEPENDENCIES) 
	@rm -f mhmm$(EXEEXT)
	$(AM_V_CCLD)$(mhmm_LINK) $(mhmm_OBJECTS) $(mhmm_LDADD) $(LIBS)

mhmm-io$(EXEEXT): $(mhmm_io_OBJECTS) $(mhmm_io_DEPENDENCIES) $(EXTRA_mhmm_io_DEPENDENCIES) 
	@rm -f mhmm-io$(EXEEXT)
	$(AM_V_CCLD)$(mhmm_io_LINK) $(mhmm_io_OBJECTS) $(mhmm_io_LDADD) $(LIBS)

mhmme$(EXEEXT): $(mhmme_OBJECTS) $(mhmme_DEPENDENCIES) $(EXTRA_mhmme_DEPENDENCIES) 
	@rm -f mhmme$(EXEEXT)
	$(AM_V_CCLD)$(mhmme_LINK) $(mhmme_OBJECTS) $(mhmme_LDADD) $(LIBS)

mhmms$(EXEEXT): $(mhmms_OBJECTS) $(mhmms_DEPENDENCIES) $(EXTRA_mhmms_DEPENDENCIES) 
	@rm -f mhmms$(EXEEXT)
	$(AM_V_CCLD)$(mhmms_LINK) $(mhmms_OBJECTS) $(mhmms_LDADD) $(LIBS)

mhmmscan$(EXEEXT): $(mhmmscan_OBJECTS) $(mhmmscan_DEPENDENCIES) $(EXTRA_mhmmscan_DEPENDENCIES) 
	@rm -f mhmmscan$(EXEEXT)
	$(AM_V_CCLD)$(mhmmscan_LINK) $(mhmmscan_OBJECTS) $(mhmmscan_LDADD) $(LIBS)

momo$(EXEEXT): $(momo_OBJECTS) $(momo_DEPENDENCIES) $(EXTRA_momo_DEPENDENCIES) 
	@rm -f momo$(EXEEXT)
	$(AM_V_CCLD)$(momo_LINK) $(momo_OBJECTS) $(momo_LDADD) $(LIBS)

motif-shuffle-columns$(EXEEXT): $(motif_shuffle_columns_OBJECTS) $(motif_shuffle_columns_DEPENDENCIES) $(EXTRA_motif_shuffle_columns_DEPENDENCIES) 
	@rm -f motif-shuffle-columns$(EXEEXT)
	$(AM_V_CCLD)$(motif_shuffle_columns_LINK) $(motif_shuffle_columns_OBJECTS) $(motif_shuffle_columns_LDADD) $(LIBS)

motiph$(EXEEXT): $(motiph_OBJECTS) $(motiph_DEPENDENCIES) $(EXTRA_motiph_DEPENDENCIES) 
	@rm -f motiph$(EXEEXT)
	$(AM_V_CCLD)$(motiph_LINK) $(motiph_OBJECTS) $(motiph_LDADD) $(LIBS)

pmp_bf$(EXEEXT): $(pmp_bf_OBJECTS) $(pmp_bf_DEPENDENCIES) $(EXTRA_pmp_bf_DEPENDENCIES) 
	@rm -f pmp_bf$(EXEEXT)
	$(AM_V_CCLD)$(pmp_bf_LINK) $(pmp_bf_OBJECTS) $(pmp_bf_LDADD) $(LIBS)

qvalue$(EXEEXT): $(qvalue_OBJECTS) $(qvalue_DEPENDENCIES) $(EXTRA_qvalue_DEPENDENCIES) 
	@rm -f qvalue$(EXEEXT)
	$(AM_V_CCLD)$(qvalue_LINK) $(qvalue_OBJECTS) $(qvalue_LDADD) $(LIBS)

ramen$(EXEEXT): $(ramen_OBJECTS) $(ramen_DEPENDENCIES) $(EXTRA_ramen_DEPENDENCIES) 
	@rm -f ramen$(EXEEXT)
	$(AM_V_CCLD)$(ramen_LINK) $(ramen_OBJECTS) $(ramen_LDADD) $(LIBS)

ranksum_test$(EXEEXT): $(ranksum_test_OBJECTS) $(ranksum_test_DEPENDENCIES) $(EXTRA_ranksum_test_DEPENDENCIES) 
	@rm -f ranksum_test$(EXEEXT)
	$(AM_V_CCLD)$(ranksum_test_LINK) $(ranksum_test_OBJECTS) $(ranksum_test_LDADD) $(LIBS)

reconcile-tree-alignment$(EXEEXT): $(reconcile_tree_alignment_OBJECTS) $(reconcile_tree_alignment_DEPENDENCIES) $(EXTRA_reconcile_tree_alignment_DEPENDENCIES) 
	@rm -f reconcile-tree-alignment$(EXEEXT)
	$(AM_V_CCLD)$(reconcile_tree_alignment_LINK) $(reconcile_tree_alignment_OBJECTS) $(reconcile_tree_alignment_LDADD) $(LIBS)

reduce-alignment$(EXEEXT): $(reduce_alignment_OBJECTS) $(reduce_alignment_DEPENDENCIES) $(EXTRA_reduce_alignment_DEPENDENCIES) 
	@rm -f reduce-alignment$(EXEEXT)
	$(AM_V_CCLD)$(reduce_alignment_LINK) $(reduce_alignment_OBJECTS) $(reduce_alignment_LDADD) $(LIBS)

remove-alignment-gaps$(EXEEXT): $(remove_alignment_gaps_OBJECTS) $(remove_alignment_gaps_DEPENDENCIES) $(EXTRA_remove_alignment_gaps_DEPENDENCIES) 
	@rm -f remove-alignment-gaps$(EXEEXT)
	$(AM_V_CCLD)$(remove_alignment_gaps_LINK) $(remove_alignment_gaps_OBJECTS) $(remove_alignment_gaps_LDADD) $(LIBS)

shadow$(EXEEXT): $(shadow_OBJECTS) $(shadow_DEPENDENCIES) $(EXTRA_shadow_DEPENDENCIES) 
	@rm -f shadow$(EXEEXT)
	$(AM_V_CCLD)$(shadow_LINK) $(shadow_OBJECTS) $(shadow_LDADD) $(LIBS)

spamo$(EXEEXT): $(spamo_OBJECTS) $(spamo_DEPENDENCIES) $(EXTRA_spamo_DEPENDENCIES) 
	@rm -f spamo$(EXEEXT)
	$(AM_V_CCLD)$(spamo_LINK) $(spamo_OBJECTS) $(spamo_LDADD) $(LIBS)

streme$(EXEEXT): $(streme_OBJECTS) $(streme_DEPENDENCIES) $(EXTRA_streme_DEPENDENCIES) 
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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-fasta-get-markov.lo: fasta-get-markov.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-gtf.lo: gtf.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-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-log_erfc.lo: log_erfc.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-match.lo: match.c
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libcommon_la-matrix.lo: matrix.c
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libcommon_la-meme-sax.lo: meme-sax.c
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libcommon_la-metameme.lo: metameme.c
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libcommon_la-mhmm.lo: mhmm.c
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libcommon_la-mhmms.lo: mhmms.c
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libcommon_la-mhmmscan.lo: mhmmscan.c
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libcommon_la-mhmm-state.lo: mhmm-state.c
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libcommon_la-momo-algorithm.lo: momo-algorithm.c
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libcommon_la-momo-input.lo: momo-input.c
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libcommon_la-momo-modl.lo: momo-modl.c
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libcommon_la-momo-motifx.lo: momo-motifx.c
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libcommon_la-momo-output.lo: momo-output.c
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libcommon_la-momo-simple.lo: momo-simple.c
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libcommon_la-motif.lo: motif.c
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libcommon_la-motif-db.lo: motif-db.c
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libcommon_la-motif-in.lo: motif-in.c
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libcommon_la-motif-in-common.lo: motif-in-common.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-random-variate.lo: random-variate.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-streme-sax.lo: streme-sax.c
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libcommon_la-streme-utils.lo: streme-utils.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-ushuffle.lo: ushuffle.c
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libcommon_la-xlate-in.lo: xlate-in.c
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libcommon_la-inputmultiseq.lo: inputmultiseq.c
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libcommon_la-st_mapfile.lo: st_mapfile.c
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libcommon_la-st_seterror.lo: st_seterror.c
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libcommon_la-st_space.lo: st_space.c
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libcommon_la-banner.lo: banner.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_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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	-rm -f ./$(DEPDIR)/libcommon_la-gendb.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-gtf-io.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-gtf.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-hash_table.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-heap.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-html-data.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-html-monolith.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-inputmultiseq.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-io.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-json-checker.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-json-reader.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-json-writer.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-karlin.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-linked-list.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-log-hmm.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-log_erfc.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-logodds.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-mast-util.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-match.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-matrix.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-mcast-match.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-meme-sax.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-metameme.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-mhmm-state.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-mhmm.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-mhmms.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-mhmmscan.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-momo-algorithm.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-momo-input.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-momo-modl.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-momo-motifx.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-momo-output.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-momo-simple.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-motif-db.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-motif-in-common.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-motif-in-dreme-xml.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-motif-in-meme-html.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-motif-in-meme-json.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-motif-in-meme-text.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-motif-in-meme-xml.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-motif-in-streme-xml.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-motif-in.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-motif.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-motif_regexp.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-motiph-scoring.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-mtwist.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-object-list.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-order.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-parser-message.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-prealigned-io.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-prior-dist.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-prior-reader-from-psp.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-prior-reader-from-wig.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-pssm-distr.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-pssm.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-qvalue.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-random-variate.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-ranksum_test.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-rdb-matrix.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-read-mhmm.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-read_sequence.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-red-black-tree.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-regex-utils.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-regress.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-reservoir.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-sax-parser-utils.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-scanned-sequence.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-scored-sites.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-seq-reader-from-fasta.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-seq.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-simple-getopt.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-spearman-rank-correlation.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-st_access.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-st_construct.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-st_dfs.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-st_mapfile.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-st_seterror.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-st_space.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-streme-sax.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-streme-utils.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-string-builder.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-string-list.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-string-match.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-subst-matrix.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-substmatrix-table.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-transfac.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-tree.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-ushuffle.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-utils.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-wiggle-reader.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-write-mhmm.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-xlate-in.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-xml-out.Plo
	-rm -f ./$(DEPDIR)/libcommon_la-xml-util.Plo
	-rm -f ./$(DEPDIR)/llr-llr.Po
	-rm -f ./$(DEPDIR)/llr-logs.Po
	-rm -f ./$(DEPDIR)/mast-diagram.Po
	-rm -f ./$(DEPDIR)/mast-mast.Po
	-rm -f ./$(DEPDIR)/mcast-mcast.Po
	-rm -f ./$(DEPDIR)/meme2alph-meme2alph.Po
	-rm -f ./$(DEPDIR)/meme2images-meme2images.Po
	-rm -f ./$(DEPDIR)/meme2meme-meme2meme.Po
	-rm -f ./$(DEPDIR)/meme_get_motif-meme-get-motif.Po
	-rm -f ./$(DEPDIR)/mhmm-mhmm.Po
	-rm -f ./$(DEPDIR)/mhmm_io-mhmm-io.Po
	-rm -f ./$(DEPDIR)/mhmme-mhmme.Po
	-rm -f ./$(DEPDIR)/mhmms-mhmms.Po
	-rm -f ./$(DEPDIR)/mhmmscan-mhmmscan.Po
	-rm -f ./$(DEPDIR)/momo-fisher_exact.Po
	-rm -f ./$(DEPDIR)/momo-momo.Po
	-rm -f ./$(DEPDIR)/motif_shuffle_columns-motif-shuffle-columns.Po
	-rm -f ./$(DEPDIR)/motiph-motiph.Po
	-rm -f ./$(DEPDIR)/pmp_bf-pmp_bf.Po
	-rm -f ./$(DEPDIR)/qvalue-qvalue.Po
	-rm -f ./$(DEPDIR)/ramen-ramen.Po
	-rm -f ./$(DEPDIR)/ramen-ramen_scan.Po
	-rm -f ./$(DEPDIR)/ranksum_test-ranksum_test.Po
	-rm -f ./$(DEPDIR)/reconcile_tree_alignment-reconcile-tree-alignment.Po
	-rm -f ./$(DEPDIR)/reduce_alignment-reduce-alignment.Po
	-rm -f ./$(DEPDIR)/remove_alignment_gaps-remove-alignment-gaps.Po
	-rm -f ./$(DEPDIR)/shadow-shadow.Po
	-rm -f ./$(DEPDIR)/spamo-cisml-sax.Po
	-rm -f ./$(DEPDIR)/spamo-spamo-matches.Po
	-rm -f ./$(DEPDIR)/spamo-spamo-output.Po
	-rm -f ./$(DEPDIR)/spamo-spamo-scan.Po
	-rm -f ./$(DEPDIR)/spamo-spamo.Po
	-rm -f ./$(DEPDIR)/streme-fisher_exact.Po
	-rm -f ./$(DEPDIR)/streme-streme.Po
	-rm -f ./$(DEPDIR)/tgene-tgene.Po
	-rm -f ./$(DEPDIR)/tomtom-tomtom.Po
	-rm -f ./$(DEPDIR)/tree-tree.Po
	-rm -f ./$(DEPDIR)/xlate_in-parser-message.Po
	-rm -f ./$(DEPDIR)/xlate_in-xlate-in.Po
	-rm -f Makefile
maintainer-clean-am: distclean-am maintainer-clean-generic

mostlyclean: mostlyclean-recursive

mostlyclean-am: mostlyclean-compile mostlyclean-generic \
	mostlyclean-libtool

pdf: pdf-recursive

pdf-am:

ps: ps-recursive

ps-am:

uninstall-am: uninstall-binPROGRAMS uninstall-memelibexecPROGRAMS

.MAKE: $(am__recursive_targets) all check install install-am \
	install-exec install-strip

.PHONY: $(am__recursive_targets) CTAGS GTAGS TAGS all all-am \
	am--depfiles check check-am clean clean-binPROGRAMS \
	clean-generic clean-libtool clean-memelibexecPROGRAMS \
	clean-noinstLTLIBRARIES cscopelist-am ctags ctags-am distclean \
	distclean-compile distclean-generic distclean-libtool \
	distclean-tags distdir dvi dvi-am html html-am info info-am \
	install install-am install-binPROGRAMS install-data \
	install-data-am install-dvi install-dvi-am install-exec \
	install-exec-am install-html install-html-am install-info \
	install-info-am install-man install-memelibexecPROGRAMS \
	install-pdf install-pdf-am install-ps install-ps-am \
	install-strip installcheck installcheck-am installdirs \
	installdirs-am maintainer-clean maintainer-clean-generic \
	mostlyclean mostlyclean-compile mostlyclean-generic \
	mostlyclean-libtool pdf pdf-am ps ps-am tags tags-am uninstall \
	uninstall-am uninstall-binPROGRAMS \
	uninstall-memelibexecPROGRAMS

.PRECIOUS: Makefile


dir.h: Makefile
	echo '#define MEME_DIR "$(prefix)"' >$@
	echo '#define DATA_DIR "$(memedatadir)" ' >> $@  
	echo '#define BIN_DIR "$(bindir)" ' >> $@
	echo '#define LIBEXEC_DIR "$(memelibexecdir)" ' >> $@
	echo '#define TEMP_DIR "$(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:
