├── ARCHIVE_DATE ├── ARCHIVE_REVISION ├── AUTHORS ├── COPYING ├── ChangeLog ├── INSTALL ├── Makefile.am ├── Makefile.in ├── MemeSuite.properties.in ├── NEWS ├── README ├── aclocal.m4 ├── config.h.in ├── config ├── ._config.guess ├── ._config.sub ├── ._install-sh ├── compile ├── config.guess ├── config.sub ├── depcomp ├── install-sh ├── ltmain.sh ├── missing └── mkinstalldirs ├── configure ├── configure.ac ├── doc ├── GLAM2_method.pdf ├── Makefile.am ├── Makefile.in ├── alphabet-format.html ├── alphabets.html ├── alphtype.html ├── ama-qvalues.html ├── ama.html ├── ame-tutorial.html ├── ame.html ├── authors.html ├── beadstring.html ├── beeml2meme.html ├── bfile-format.html ├── centrimo-tutorial.html ├── centrimo.html ├── ceqlogo.html ├── chen2meme.html ├── cite.html ├── clustalw-format.html ├── clustalw2fasta.html ├── clustalw2phylip.html ├── compute-prior-dist.html ├── compute-uniform-priors.html ├── copyright.html ├── copyright.html.in ├── create-priors.html ├── css │ ├── Makefile.am │ ├── Makefile.in │ ├── menu.css │ └── style.css ├── dmix-format.html ├── download.html ├── draw-mhmm.html ├── dreme-tutorial.html ├── dreme.html ├── dust.html ├── elm2meme.html ├── examples │ ├── Makefile.am │ ├── Makefile.in │ ├── ame_example_output_files │ │ ├── ame.html │ │ └── ame.txt │ ├── centrimo_example_output_files │ │ ├── centrimo.html │ │ ├── centrimo.txt │ │ └── site_counts.txt │ ├── compute_prior_dist_example_output_files │ │ ├── Makefile.am │ │ ├── Makefile.in │ │ └── prior.dist.txt │ ├── dreme_example_output_files │ │ ├── dreme.html │ │ ├── dreme.txt │ │ ├── dreme.xml │ │ ├── m01nc_CCMCRCCC.png │ │ ├── m01rc_GGGYGKGG.png │ │ ├── m02nc_BTTATCW.png │ │ ├── m02rc_WGATAAV.png │ │ ├── m03nc_MCRCCCA.png │ │ ├── m03rc_TGGGYGK.png │ │ ├── m04nc_RARGAAA.png │ │ ├── m04rc_TTTCYTY.png │ │ ├── m05nc_AKAAAM.png │ │ ├── m05rc_KTTTMT.png │ │ ├── m06nc_CTGTSTS.png │ │ ├── m06rc_SASACAG.png │ │ ├── m07nc_AGGGCGK.png │ │ ├── m07rc_MCGCCCT.png │ │ ├── m08nc_CCTKCCY.png │ │ ├── m08rc_RGGMAGG.png │ │ ├── m09nc_TTAAAAW.png │ │ ├── m09rc_WTTTTAA.png │ │ ├── m10nc_AAATAH.png │ │ ├── m10rc_DTATTT.png │ │ ├── m11nc_CATYTCC.png │ │ ├── m11rc_GGARATG.png │ │ ├── m12nc_CAGMCAC.png │ │ ├── m12rc_GTGKCTG.png │ │ ├── m13nc_CACAGY.png │ │ ├── m13rc_RCTGTG.png │ │ ├── m14nc_CTGGRGA.png │ │ ├── m14rc_TCYCCAG.png │ │ ├── m15nc_SACGTGA.png │ │ └── m15rc_TCACGTS.png │ ├── examples.mk │ ├── fimo_example_output_files │ │ ├── cisml.xml │ │ ├── fimo.gff │ │ ├── fimo.html │ │ ├── fimo.txt │ │ └── fimo.xml │ ├── glam2_example_output_files │ │ ├── glam2.html │ │ ├── glam2.meme │ │ ├── glam2.txt │ │ ├── logo1.eps │ │ ├── logo1.png │ │ ├── logo10.eps │ │ ├── logo10.png │ │ ├── logo2.eps │ │ ├── logo2.png │ │ ├── logo3.eps │ │ ├── logo3.png │ │ ├── logo4.eps │ │ ├── logo4.png │ │ ├── logo5.eps │ │ ├── logo5.png │ │ ├── logo6.eps │ │ ├── logo6.png │ │ ├── logo7.eps │ │ ├── logo7.png │ │ ├── logo8.eps │ │ ├── logo8.png │ │ ├── logo9.eps │ │ ├── logo9.png │ │ ├── logo_ssc1.eps │ │ ├── logo_ssc1.png │ │ ├── logo_ssc10.eps │ │ ├── logo_ssc10.png │ │ ├── logo_ssc2.eps │ │ ├── logo_ssc2.png │ │ ├── logo_ssc3.eps │ │ ├── logo_ssc3.png │ │ ├── logo_ssc4.eps │ │ ├── logo_ssc4.png │ │ ├── logo_ssc5.eps │ │ ├── logo_ssc5.png │ │ ├── logo_ssc6.eps │ │ ├── logo_ssc6.png │ │ ├── logo_ssc7.eps │ │ ├── logo_ssc7.png │ │ ├── logo_ssc8.eps │ │ ├── logo_ssc8.png │ │ ├── logo_ssc9.eps │ │ └── logo_ssc9.png │ ├── glam2scan_example_output_files │ │ ├── glam2scan.html │ │ └── glam2scan.txt │ ├── gomo_example_output_files │ │ ├── gomo.html │ │ ├── gomo.txt │ │ ├── gomo.xml │ │ └── res │ │ │ ├── logo1.png │ │ │ ├── logo2.png │ │ │ └── logo3.png │ ├── mast_example_output_files │ │ ├── mast.html │ │ ├── mast.txt │ │ └── mast.xml │ ├── mcast_example_output_files │ │ ├── cisml.xml │ │ ├── mcast.gff │ │ ├── mcast.html │ │ ├── mcast.txt │ │ └── mcast.xml │ ├── meme_example_output_files │ │ ├── logo1.eps │ │ ├── logo1.png │ │ ├── logo2.eps │ │ ├── logo2.png │ │ ├── logo3.eps │ │ ├── logo3.png │ │ ├── logo_rc1.eps │ │ ├── logo_rc1.png │ │ ├── logo_rc2.eps │ │ ├── logo_rc2.png │ │ ├── logo_rc3.eps │ │ ├── logo_rc3.png │ │ ├── meme.html │ │ ├── meme.txt │ │ └── meme.xml │ ├── memechip_example_output_files │ │ ├── Klf1.fna │ │ ├── align_msgs.txt │ │ ├── background │ │ ├── centrimo_out │ │ │ ├── centrimo.html │ │ │ ├── centrimo.txt │ │ │ └── site_counts.txt │ │ ├── combined.meme │ │ ├── dreme_out │ │ │ ├── dreme.html │ │ │ ├── dreme.txt │ │ │ ├── dreme.xml │ │ │ ├── m01nc_MCRCCCW.png │ │ │ ├── m01rc_WGGGYGK.png │ │ │ ├── m02nc_TTATCW.png │ │ │ └── m02rc_WGATAA.png │ │ ├── dreme_tomtom_out │ │ │ ├── tomtom.html │ │ │ ├── tomtom.txt │ │ │ └── tomtom.xml │ │ ├── fimo_out_1 │ │ │ ├── cisml.xml │ │ │ ├── fimo.gff │ │ │ ├── fimo.html │ │ │ ├── fimo.txt │ │ │ └── fimo.xml │ │ ├── fimo_out_2 │ │ │ ├── cisml.xml │ │ │ ├── fimo.gff │ │ │ ├── fimo.html │ │ │ ├── fimo.txt │ │ │ └── fimo.xml │ │ ├── fimo_out_3 │ │ │ ├── cisml.xml │ │ │ ├── fimo.gff │ │ │ ├── fimo.html │ │ │ ├── fimo.txt │ │ │ └── fimo.xml │ │ ├── fimo_out_4 │ │ │ ├── cisml.xml │ │ │ ├── fimo.gff │ │ │ ├── fimo.html │ │ │ ├── fimo.txt │ │ │ └── fimo.xml │ │ ├── fimo_out_5 │ │ │ ├── cisml.xml │ │ │ ├── fimo.gff │ │ │ ├── fimo.html │ │ │ ├── fimo.txt │ │ │ └── fimo.xml │ │ ├── meme-chip.html │ │ ├── meme_out │ │ │ ├── logo1.eps │ │ │ ├── logo1.png │ │ │ ├── logo2.eps │ │ │ ├── logo2.png │ │ │ ├── logo3.eps │ │ │ ├── logo3.png │ │ │ ├── logo_rc1.eps │ │ │ ├── logo_rc1.png │ │ │ ├── logo_rc2.eps │ │ │ ├── logo_rc2.png │ │ │ ├── logo_rc3.eps │ │ │ ├── logo_rc3.png │ │ │ ├── meme.html │ │ │ ├── meme.txt │ │ │ └── meme.xml │ │ ├── meme_tomtom_out │ │ │ ├── tomtom.html │ │ │ ├── tomtom.txt │ │ │ └── tomtom.xml │ │ ├── motif_alignment.txt │ │ ├── progress_log.txt │ │ ├── seqs-centered │ │ ├── seqs-discarded │ │ ├── seqs-sampled │ │ ├── seqs-shuffled │ │ ├── spamo_out_1 │ │ │ ├── spamo.html │ │ │ └── spamo.tsv │ │ ├── spamo_out_2 │ │ │ ├── spamo.html │ │ │ └── spamo.tsv │ │ ├── spamo_out_3 │ │ │ ├── spamo.html │ │ │ └── spamo.tsv │ │ ├── spamo_out_4 │ │ │ ├── spamo.html │ │ │ └── spamo.tsv │ │ ├── spamo_out_5 │ │ │ ├── spamo.html │ │ │ └── spamo.tsv │ │ └── summary.tsv │ ├── momo_example_output_files │ │ ├── S79.9.png │ │ ├── T79.9.png │ │ ├── Y79.9.png │ │ ├── momo.html │ │ └── momo.txt │ ├── motiph_example_output_files │ │ ├── cisml-to-html.xsl │ │ ├── cisml.css │ │ ├── motiph.gff │ │ ├── motiph.html │ │ ├── motiph.txt │ │ └── motiph.xml │ ├── sample-dna-aln.glam2 │ ├── sample-dna-motif.meme │ ├── sample-protein-aln.glam2 │ ├── sample-protein-motif.meme │ ├── sample_opal_scripts │ │ ├── FimoClient.pl │ │ ├── FimoClient.py │ │ ├── Makefile.am │ │ ├── Makefile.in │ │ ├── MemeClient.pl │ │ ├── MemeClient.py │ │ ├── crp0.fasta │ │ └── crp0.meme.xml │ ├── small-tide-mod.txt │ ├── spamo_example_output_files │ │ ├── spamo.html │ │ └── spamo.tsv │ └── tomtom_example_output_files │ │ ├── tomtom.html │ │ ├── tomtom.txt │ │ └── tomtom.xml ├── fasta-fetch.html ├── fasta-format.html ├── fasta-get-markov.html ├── fasta-grep.html ├── fasta-hamming-enrich.html ├── fasta-io.html ├── fasta-make-index.html ├── fasta-most.html ├── fasta-shuffle-letters.html ├── fasta-subsample.html ├── fasta-unique-names.html ├── fimo-tutorial.html ├── fimo.html ├── fisher_exact.html ├── fitevd.html ├── gendb.html ├── general-faq.html ├── getsize.html ├── glam2.html ├── glam2_alphabet.html ├── glam2_tut.html ├── glam2format.html ├── glam2mask.html ├── glam2scan.html ├── godag-format.html ├── gomo-format.html ├── gomo.html ├── gomo_highlight.html ├── images │ ├── Makefile.am │ ├── Makefile.in │ ├── UWlogo150p.gif │ ├── ame_icon.png │ ├── centrimo_icon.png │ ├── dreme_icon.png │ ├── fimo_icon.png │ ├── glam2_icon.png │ ├── glam2scan_icon.png │ ├── gomo_icon.png │ ├── gtscan_icon.png │ ├── mast_icon.png │ ├── mcast_icon.png │ ├── meme_icon.png │ ├── memechip_icon.png │ ├── memesuite_icon.ico │ ├── memesuite_icon.png │ ├── momo_icon.png │ ├── spamo_icon.png │ ├── tomtom_icon.png │ ├── ucsd_logo.png │ ├── uq_logo.png │ └── webserver_schema.png ├── install.html ├── ismb94.pdf ├── iupac.html ├── iupac2meme.html ├── jaspar2meme.html ├── js │ ├── Makefile.am │ ├── Makefile.in │ ├── Markdown.Converter.LICENSE │ ├── Markdown.Converter.js │ ├── centrimo_graph.js │ ├── delay_draw.js │ ├── eps_context.js │ ├── manual.js │ ├── menu-configure.js.in │ ├── menu-data.js │ ├── menu-path.js │ ├── menu.js │ ├── motif_logo.js │ ├── shared-doc.js │ ├── simple-shared-doc.js │ ├── spamo_graph.js │ └── utilities.js ├── log-hmm.html ├── mast.html ├── matrix2meme.html ├── mcast.html ├── meme-chip.html ├── meme-format.html ├── meme-get-motif.html ├── meme-rename.html ├── meme.html ├── meme2alph.html ├── meme2images.html ├── meme2meme.html ├── mhmm-format.html ├── mhmm.html ├── mhmm2html.html ├── mhmme.html ├── mhmms.html ├── mhmmscan-format.html ├── mhmmscan.html ├── momo.html ├── motif-consensus.html ├── motif-shuffle-columns.html ├── motif_conversion.html ├── motiph.html ├── nmica2meme.html ├── overview.html ├── pmp_bf.html ├── priority2meme.html ├── psm-format.html ├── psp-format.html ├── psp-gen.html ├── purge.html ├── qvalue.html ├── reconcile-tree-alignment.html ├── reduce-alignment.html ├── release-notes.html ├── remove-alignment-gaps.html ├── rna2meme.html ├── scpd2meme.html ├── scripting.html ├── shadow.html ├── sites2meme.html ├── spamo.html ├── taipale2meme.html ├── tamo2meme.html ├── tomtom.html ├── transfac-format.html ├── transfac2meme.html ├── uniprobe2meme.html └── update-sequence-db.html ├── etc ├── AME_config.xml.in ├── CENTRIMO_config.xml.in ├── DREME_config.xml.in ├── FIMO_config.xml.in ├── GLAM2SCAN_config.xml.in ├── GLAM2_config.xml.in ├── GOMO_config.xml.in ├── MAST_config.xml.in ├── MCAST_config.xml.in ├── MEMECHIP_config.xml.in ├── MEME_config.xml.in ├── MOMO_config.xml.in ├── Makefile.am ├── Makefile.in ├── SPAMO_config.xml.in ├── TOMTOM_config.xml.in ├── alphabet_utilities.js ├── ame_icon.png ├── ame_template.css ├── ame_template.html ├── ame_template.js ├── beadstring.xsl ├── block_diagram.css ├── block_diagram.js ├── centrimo_graph.js ├── centrimo_icon.png ├── centrimo_template.css ├── centrimo_template.html ├── centrimo_template.js ├── cisml-to-gff.xsl ├── cisml-to-gff3.xsl ├── cisml-to-html.xsl ├── cisml-to-text.xsl ├── cisml.css ├── constants.js.in ├── constants.xsl.in ├── db_general.csv ├── db_other_genomes.csv ├── delay_draw.js ├── dreme_icon.png ├── dreme_template.css ├── dreme_template.html ├── dreme_template.js ├── eps_context.js ├── fimo-to-gff3.xsl ├── fimo-to-html.xsl ├── fimo-to-text.xsl ├── fimo_icon.png ├── generate_js_wrapped_template.pl ├── generate_xsl_icons.pl ├── gomo-to-html.xsl ├── hmm-text.xsl ├── job_status.tmpl ├── logging.conf.in ├── mast_icon.png ├── mast_template.css ├── mast_template.html ├── mast_template.js ├── mcast_icon.png ├── mcast_template.css ├── mcast_template.html ├── mcast_template.js ├── meme-chip_template.css ├── meme-chip_template.html ├── meme-chip_template.js ├── meme.css ├── meme_icon.png ├── meme_template.css ├── meme_template.html ├── meme_template.js ├── memechip_icon.png ├── motif_logo.js ├── new_icon.png ├── prior1.plib ├── prior30.plib ├── spamo_graph.js ├── spamo_icon.png ├── spamo_template.css ├── spamo_template.html ├── spamo_template.js ├── template.eps ├── tomtom_icon.png ├── tomtom_template.css ├── tomtom_template.html ├── tomtom_template.js ├── utilities.js └── xsl-wrapper.in ├── m4 ├── ._libtool.m4 ├── ._ltoptions.m4 ├── ._ltsugar.m4 ├── ._lt~obsolete.m4 ├── libtool.m4 ├── ltoptions.m4 ├── ltsugar.m4 ├── ltversion.m4 └── lt~obsolete.m4 ├── scripts ├── Alphabet.pm ├── CheckingSAX.pm ├── CombDynProg.pm ├── DiffJSON.pm ├── DiffXML.pm ├── DremeSAX.pm ├── ExecUtils.pm ├── Globals.pm.in ├── HtmlMonolithWr.pm ├── HypergeometricDynProg.pm ├── JsonRdr.pm ├── JsonWr.pm ├── Makefile.am ├── Makefile.in ├── MastSAX.pm ├── MemeSAX.pm ├── MemeWebUtils.pm.in ├── MotifInDremeXML.pm ├── MotifInMemeXML.pm ├── MotifUtils.pm ├── PriorUtils.pm ├── README ├── ReadFastaFile.pm ├── StatusPage.pm.in ├── TomtomSAX.pm ├── alphabet.py ├── alphabet_py3.py ├── ama-qvalues.pl.in ├── ame_webservice.pl.in ├── beeml2meme.pl.in ├── centrimo_webservice.pl.in ├── chen2meme.pl.in ├── dependencies.pl ├── dreme.py.in ├── dreme_py3.py.in ├── dreme_webservice.pl.in ├── dreme_xml_to_html.pl.in ├── dreme_xml_to_txt.pl.in ├── elm2meme.pl.in ├── fasta-center.pl.in ├── fasta-dinucleotide-shuffle-py3.in ├── fasta-dinucleotide-shuffle.py.in ├── fasta-enriched-center.pl.in ├── fasta-fetch.pl.in ├── fasta-grep ├── fasta-hamming-enrich-py3.in ├── fasta-hamming-enrich.py.in ├── fasta-make-index.pl.in ├── fasta-most.pl.in ├── fasta-re-match.pl.in ├── fasta-subsample.pl.in ├── fasta-unique-names.pl.in ├── fimo_webservice.pl.in ├── glam2_webservice.pl.in ├── glam2html.py.in ├── glam2psfm.py.in ├── glam2scan2html.py.in ├── glam2scan_webservice.pl.in ├── gomo_webservice.pl.in ├── hart2meme-bkg.pl.in ├── hartemink2psp.pl.in ├── hypergeometric.py ├── hypergeometric_py3.py ├── iupac2meme.pl.in ├── jaspar2meme.pl.in ├── lrun.pl.in ├── mast_webservice.pl.in ├── mast_xml_to_html.pl.in ├── mast_xml_to_txt.pl.in ├── matrix2meme.pl.in ├── mcast.pl.in ├── mcast_webservice.pl.in ├── meme-chip.pl.in ├── meme-chip_html_to_tsv.pl.in ├── meme-chip_webservice.pl.in ├── meme-rename.pl.in ├── meme_webservice.pl.in ├── meme_xml_to_html.pl.in ├── mhmm2html.pl.in ├── momo_webservice.pl.in ├── nmica2meme.pl.in ├── obo2dag.jar ├── plot-usage ├── plotgen ├── priority2meme.pl.in ├── psp-gen.pl.in ├── rna2meme.pl.in ├── rsat-retrieve-seq.pl.in ├── rsat-supported-organisms.pl.in ├── scpd2meme.pl.in ├── sd ├── sequence.py ├── sequence_py3.py ├── sites2meme.pl.in ├── spamo_webservice.pl.in ├── taipale2meme.pl.in ├── tamo2meme.pl.in ├── texit.pl.in ├── tomtom_webservice.pl.in ├── tomtom_xml_to_html.pl.in ├── transfac2meme.pl.in ├── uniprobe2meme.pl.in ├── update-plot-usage.pl.in ├── update-sequence-db.sh.in └── usage-reports ├── src ├── Makefile.am ├── Makefile.in ├── aa.h ├── align.h ├── alignment.c ├── alignment.h ├── alph-in.c ├── alph-in.h ├── alphabet.c ├── alphabet.h ├── alphtype.c ├── ama.c ├── ame.c ├── ame.h ├── array-list.c ├── array-list.h ├── array.c ├── array.h ├── banner.c ├── banner.h ├── beadstring-xml.h ├── beadstring.c ├── beadstring.h ├── binary-search.c ├── binary-search.h ├── binomial.c ├── binomial.h ├── branching_search.c ├── buffer.c ├── buffer.h ├── build-hmm.c ├── build-hmm.h ├── calculate_p_y.c ├── calculate_p_y.h ├── centrimo.c ├── ceqlogo.c ├── ceqlogo.h ├── cisml-dtd.h ├── cisml-sax.c ├── cisml-sax.h ├── cisml.c ├── cisml.h ├── clustalw-io.c ├── clustalw-io.h ├── clustalw2fasta.c ├── clustalw2phylip.c ├── compute-prior-dist.c ├── compute-uniform-priors.c ├── create-priors.c ├── curves.h ├── data-block-reader.c ├── data-block-reader.h ├── data-block.c ├── data-block.h ├── diagram.c ├── diagram.h ├── discretize.c ├── display.c ├── display.h ├── display_globals.h ├── dp.c ├── dp.h ├── dpalign.c ├── dpalign.h ├── draw-mhmm.c ├── dreme-sax.c ├── dreme-sax.h ├── em.c ├── em.h ├── empirical-qvalue.c ├── empirical-qvalue.h ├── eps2png.c ├── eps2png.h ├── evomodel.c ├── evomodel.h ├── exec_parallel.c ├── fasta-get-markov.c ├── fasta-io.c ├── fasta-io.h ├── fasta-shuffle-letters.c ├── filters │ ├── Makefile.am │ ├── Makefile.in │ ├── dust │ │ ├── Makefile.am │ │ ├── Makefile.in │ │ ├── README │ │ ├── dust.c │ │ ├── getfa.c │ │ ├── getfa.h │ │ └── tust.c │ └── purge │ │ ├── Makefile.am │ │ ├── Makefile.in │ │ ├── README │ │ ├── afnio.c │ │ ├── afnio.h │ │ ├── alphabet.c │ │ ├── alphabet.h │ │ ├── block.c │ │ ├── block.h │ │ ├── dheap.c │ │ ├── dheap.h │ │ ├── gblast.c │ │ ├── gblast.h │ │ ├── karlin.c │ │ ├── karlin.h │ │ ├── mheap.c │ │ ├── mheap.h │ │ ├── mlist.c │ │ ├── mlist.h │ │ ├── pairaln.c │ │ ├── pairaln.h │ │ ├── pmain.c │ │ ├── purge.c │ │ ├── purge.h │ │ ├── random.c │ │ ├── random.h │ │ ├── residues.h │ │ ├── seqset.c │ │ ├── seqset.h │ │ ├── sequence.c │ │ ├── sequence.h │ │ └── stdinc.h ├── fimo-html-string.h ├── fimo-output.c ├── fimo-output.h ├── fimo.c ├── fimo.h ├── fisher_exact.c ├── fisher_exact.h ├── fitevd.c ├── fitevd.h ├── gendb.c ├── gendb.h ├── general.h ├── getsize.c ├── glam2_alignment.c ├── glam2_alignment.h ├── glam2_alphabet.c ├── glam2_alphabet.h ├── glam2_args.c ├── glam2_args.h ├── glam2_column_sample.c ├── glam2_column_sample.h ├── glam2_convolve.h ├── glam2_dirichlet.c ├── glam2_dirichlet.h ├── glam2_dna_prior.c ├── glam2_dna_prior.h ├── glam2_fasta.c ├── glam2_fasta.h ├── glam2_glam2.c ├── glam2_glam2.h ├── glam2_glam2_aln.c ├── glam2_glam2_aln.h ├── glam2_glam2format.c ├── glam2_glam2mask.c ├── glam2_heap.c ├── glam2_heap.h ├── glam2_init.c ├── glam2_init.h ├── glam2_motif.c ├── glam2_motif.h ├── glam2_output.c ├── glam2_output.h ├── glam2_recode3_20comp.c ├── glam2_recode3_20comp.h ├── glam2_scan.c ├── glam2_scan.h ├── glam2_scan_args.c ├── glam2_scan_args.h ├── glam2_scan_init.c ├── glam2_scan_init.h ├── glam2_scan_output.c ├── glam2_scan_output.h ├── glam2_site_sample.c ├── glam2_site_sample.h ├── glam2_util.c ├── glam2_util.h ├── glam2_version.h ├── gomo.c ├── gomo_highlight.c ├── gomo_highlight.h ├── hash.h ├── hash_table.c ├── hash_table.h ├── hash_table_string.h ├── heap.c ├── heap.h ├── histogram.h ├── html-data.c ├── html-data.h ├── html-monolith.c ├── html-monolith.h ├── ic.h ├── import-html-template.c ├── init.c ├── io.c ├── io.h ├── json-checker.c ├── json-checker.h ├── json-reader.c ├── json-reader.h ├── json-writer.c ├── json-writer.h ├── justlike.c ├── karlin.c ├── karlin.h ├── libexslt │ ├── Makefile.am │ ├── Makefile.in │ ├── common.c │ ├── crypto.c │ ├── date.c │ ├── dynamic.c │ ├── exslt.c │ ├── exslt.h │ ├── exsltconfig.h │ ├── exsltexports.h │ ├── functions.c │ ├── libexslt.h │ ├── math.c │ ├── saxon.c │ ├── sets.c │ └── strings.c ├── libxml2 │ ├── Copyright │ ├── DOCBparser.c │ ├── HTMLparser.c │ ├── HTMLtree.c │ ├── Makefile.am │ ├── Makefile.in │ ├── SAX.c │ ├── SAX2.c │ ├── c14n.c │ ├── catalog.c │ ├── chvalid.c │ ├── debugXML.c │ ├── dict.c │ ├── elfgcchack.h │ ├── encoding.c │ ├── entities.c │ ├── error.c │ ├── globals.c │ ├── hash.c │ ├── include │ │ ├── Makefile.am │ │ ├── Makefile.in │ │ ├── libxml │ │ │ ├── DOCBparser.h │ │ │ ├── HTMLparser.h │ │ │ ├── HTMLtree.h │ │ │ ├── Makefile.am │ │ │ ├── Makefile.in │ │ │ ├── SAX.h │ │ │ ├── SAX2.h │ │ │ ├── c14n.h │ │ │ ├── catalog.h │ │ │ ├── chvalid.h │ │ │ ├── debugXML.h │ │ │ ├── dict.h │ │ │ ├── encoding.h │ │ │ ├── entities.h │ │ │ ├── globals.h │ │ │ ├── hash.h │ │ │ ├── list.h │ │ │ ├── nanoftp.h │ │ │ ├── nanohttp.h │ │ │ ├── parser.h │ │ │ ├── parserInternals.h │ │ │ ├── pattern.h │ │ │ ├── relaxng.h │ │ │ ├── schemasInternals.h │ │ │ ├── schematron.h │ │ │ ├── threads.h │ │ │ ├── tree.h │ │ │ ├── uri.h │ │ │ ├── valid.h │ │ │ ├── xinclude.h │ │ │ ├── xlink.h │ │ │ ├── xmlIO.h │ │ │ ├── xmlautomata.h │ │ │ ├── xmlerror.h │ │ │ ├── xmlexports.h │ │ │ ├── xmlmemory.h │ │ │ ├── xmlmodule.h │ │ │ ├── xmlreader.h │ │ │ ├── xmlregexp.h │ │ │ ├── xmlsave.h │ │ │ ├── xmlschemas.h │ │ │ ├── xmlschemastypes.h │ │ │ ├── xmlstring.h │ │ │ ├── xmlunicode.h │ │ │ ├── xmlversion.h │ │ │ ├── xmlwriter.h │ │ │ ├── xpath.h │ │ │ ├── xpathInternals.h │ │ │ └── xpointer.h │ │ ├── win32config.h │ │ └── wsockcompat.h │ ├── legacy.c │ ├── libxml.h │ ├── list.c │ ├── ltmain.sh │ ├── nanoftp.c │ ├── nanohttp.c │ ├── parser.c │ ├── parserInternals.c │ ├── pattern.c │ ├── relaxng.c │ ├── schematron.c │ ├── threads.c │ ├── tree.c │ ├── trio.c │ ├── trio.h │ ├── triodef.h │ ├── trionan.c │ ├── trionan.h │ ├── triop.h │ ├── triostr.c │ ├── triostr.h │ ├── uri.c │ ├── valid.c │ ├── xinclude.c │ ├── xlink.c │ ├── xmlIO.c │ ├── xmlmemory.c │ ├── xmlmodule.c │ ├── xmlreader.c │ ├── xmlregexp.c │ ├── xmlsave.c │ ├── xmlschemas.c │ ├── xmlschemastypes.c │ ├── xmlstring.c │ ├── xmlunicode.c │ ├── xmlwriter.c │ ├── xpath.c │ └── xpointer.c ├── libxslt │ ├── Copyright │ ├── Makefile.am │ ├── Makefile.in │ ├── attributes.c │ ├── attributes.h │ ├── attrvt.c │ ├── documents.c │ ├── documents.h │ ├── extensions.c │ ├── extensions.h │ ├── extra.c │ ├── extra.h │ ├── functions.c │ ├── functions.h │ ├── imports.c │ ├── imports.h │ ├── keys.c │ ├── keys.h │ ├── libxslt.h │ ├── namespaces.c │ ├── namespaces.h │ ├── numbers.c │ ├── numbersInternals.h │ ├── pattern.c │ ├── pattern.h │ ├── preproc.c │ ├── preproc.h │ ├── security.c │ ├── security.h │ ├── templates.c │ ├── templates.h │ ├── transform.c │ ├── transform.h │ ├── variables.c │ ├── variables.h │ ├── win32config.h │ ├── xslt.c │ ├── xslt.h │ ├── xsltInternals.h │ ├── xsltconfig.h │ ├── xsltexports.h │ ├── xsltlocale.c │ ├── xsltlocale.h │ ├── xsltutils.c │ ├── xsltutils.h │ ├── xsltwin32config.h │ └── xsltwin32config.h.in ├── likelihood.c ├── linked-list.c ├── linked-list.h ├── llr.c ├── llr.h ├── log-hmm.c ├── log-hmm.h ├── logodds.c ├── logodds.h ├── logs.c ├── logs.h ├── macros.h ├── mast-util.c ├── mast.c ├── mast.h ├── match.c ├── match.h ├── matrix.c ├── matrix.h ├── mcast-match.c ├── mcast-match.h ├── mcast.c ├── meme-dtd.h ├── meme-get-motif.c ├── meme-sax.c ├── meme-sax.h ├── meme.c ├── meme.h ├── meme2alph.c ├── meme2images.c ├── meme2meme.c ├── meme_util.c ├── merger.c ├── merger.h ├── message.c ├── message.h ├── meta-pssm-distr.h ├── metameme.c ├── metameme.h ├── mhmm-dtd.h ├── mhmm-io.c ├── mhmm-state.c ├── mhmm-state.h ├── mhmm.c ├── mhmm.h ├── mhmme.c ├── mhmms.c ├── mhmms.h ├── mhmmscan.c ├── mhmmscan.h ├── momo-algorithm.c ├── momo-algorithm.h ├── momo-html-string.h ├── momo-input.c ├── momo-input.h ├── momo-modl.c ├── momo-modl.h ├── momo-motifx.c ├── momo-motifx.h ├── momo-output.c ├── momo-output.h ├── momo-simple.c ├── momo-simple.h ├── momo.c ├── momo.h ├── motif-in-common.c ├── motif-in-common.h ├── motif-in-dreme-xml.c ├── motif-in-dreme-xml.h ├── motif-in-flags.h ├── motif-in-meme-html.c ├── motif-in-meme-html.h ├── motif-in-meme-json.c ├── motif-in-meme-json.h ├── motif-in-meme-text.c ├── motif-in-meme-text.h ├── motif-in-meme-xml.c ├── motif-in-meme-xml.h ├── motif-in.c ├── motif-in.h ├── motif-shuffle-columns.c ├── motif-spec.h ├── motif.c ├── motif.h ├── motif_regexp.c ├── motif_regexp.h ├── motifs.c ├── motifs.h ├── motiph-scoring.c ├── motiph-scoring.h ├── motiph.c ├── mp.c ├── mp.h ├── mtwist.c ├── mtwist.h ├── mtype.h ├── nrutil.h ├── object-list.c ├── object-list.h ├── oops.c ├── order.c ├── order.h ├── parallel │ ├── Makefile.am │ └── Makefile.in ├── params.h ├── parser-message.c ├── parser-message.h ├── partition.c ├── partition.h ├── pmp_bf.c ├── prealigned-io.c ├── prealigned-io.h ├── prior-dist.c ├── prior-dist.h ├── prior-reader-from-psp.c ├── prior-reader-from-psp.h ├── prior-reader-from-wig.c ├── prior-reader-from-wig.h ├── prior.c ├── prior.h ├── psp.c ├── psp.h ├── pssm-distr.c ├── pssm-distr.h ├── pssm.c ├── pssm.h ├── qvalue.c ├── qvalue.h ├── ramen.c ├── ramen_scan.c ├── ramen_scan.h ├── ranksum_test.c ├── ranksum_test.h ├── rdb-matrix.c ├── rdb-matrix.h ├── read-mhmm.c ├── read-mhmm.h ├── read_csv.c ├── read_csv.h ├── read_seq_file.c ├── read_seq_file.h ├── read_sequence.c ├── read_sequence.h ├── reconcile-tree-alignment.c ├── red-black-tree.c ├── red-black-tree.h ├── reduce-alignment.c ├── regex-utils.c ├── regex-utils.h ├── regress.c ├── regress.h ├── remove-alignment-gaps.c ├── reservoir.c ├── reservoir.h ├── sax-parser-utils.c ├── sax-parser-utils.h ├── scanned-sequence.c ├── scanned-sequence.h ├── scored-sites.c ├── scored-sites.h ├── seed.c ├── seed.h ├── seed_diffs.c ├── seed_diffs.h ├── seq-reader-from-fasta.c ├── seq-reader-from-fasta.h ├── seq.c ├── seq.h ├── seq2theta.c ├── shadow.c ├── shuffle_int.h ├── simple-getopt.c ├── simple-getopt.h ├── sp_matrix.c ├── sp_matrix.h ├── spamo-cisml.h ├── spamo-matches.c ├── spamo-matches.h ├── spamo-output.c ├── spamo-output.h ├── spamo-scan.c ├── spamo-scan.h ├── spamo.c ├── spearman-rank-correlation.c ├── spearman-rank-correlation.h ├── split.h ├── star.h ├── starts.c ├── string-builder.c ├── string-builder.h ├── string-list.c ├── string-list.h ├── string-match.c ├── string-match.h ├── strlcpy.h ├── subseq7.c ├── subst-matrix.c ├── subst-matrix.h ├── substmatrix-table.c ├── substmatrix-table.h ├── tcm.c ├── tomtom.c ├── transfac.c ├── transfac.h ├── tree.c ├── tree.h ├── user.h ├── ushuffle.c ├── ushuffle.h ├── utest.h ├── utils.c ├── utils.h ├── verbosity.c ├── wiggle-reader.c ├── wiggle-reader.h ├── write-mhmm.c ├── write-mhmm.h ├── xlate-in.c ├── xlate-in.h ├── xml-out.c ├── xml-out.h ├── xml-util.c ├── xml-util.h ├── xsltproc_lite.c └── zscore.h ├── tests ├── Makefile.am ├── Makefile.in ├── ame │ ├── Makefile.am │ ├── Makefile.in │ └── ame.txt ├── centrimo │ ├── Makefile.am │ ├── Makefile.in │ ├── centrimo.html │ ├── centrimo.txt │ ├── dreme-Klf1.xml │ └── site_counts.txt ├── clustalw2fasta │ ├── Makefile.am │ ├── Makefile.in │ ├── test.consensus.fasta │ ├── test.fasta │ └── test.nogap.fasta ├── common │ ├── At.s │ ├── INO_up800.s │ ├── Jaspar-subset.meme │ ├── Klf1-200-100-shuffled.s │ ├── Klf1-200-100.s │ ├── Klf1-200.s │ ├── Klf1.s │ ├── MCM1.fasta │ ├── Makefile.am │ ├── Makefile.in │ ├── Puf3p-20.s │ ├── Puf3p-200.s │ ├── Puf3p.s │ ├── adh.s │ ├── alphabet_dna.txt │ ├── alphabet_rna.txt │ ├── chr22.fasta │ ├── crp0-test.fasta │ ├── crp0.fasta │ ├── crp0.meme.html │ ├── crp0.meme.txt │ ├── crp0.meme.xml │ ├── crp0.s │ ├── dros.fasta │ ├── dros.oops.html │ ├── extended_dna.alph │ ├── farntrans5.s │ ├── lex0.s │ ├── lipo-test.fasta │ ├── lipo.fasta │ ├── lipo.meme.html │ ├── lipo.meme.old.html │ ├── lipocalin.s │ ├── mini-drosoph.s │ ├── motif.Puf3p │ │ ├── Makefile.am │ │ ├── Makefile.in │ │ ├── dreme.html │ │ ├── dreme.txt │ │ ├── dreme.xml │ │ ├── meme.html │ │ ├── meme.txt │ │ └── meme.xml │ ├── motif.crp0 │ │ ├── Makefile.am │ │ ├── Makefile.in │ │ ├── dreme.html │ │ ├── dreme.txt │ │ ├── dreme.xml │ │ ├── meme.html │ │ ├── meme.txt │ │ └── meme.xml │ ├── noq.s │ ├── nr.freq │ ├── nt.freq │ ├── psp_test.psp │ ├── psp_test.s │ ├── sample.meme │ ├── simple.aln │ ├── simple.meme │ ├── test.aln │ ├── test_tree.txt │ ├── uprot.freq │ ├── yeast.nc.1.freq │ ├── yeast.nc.3.freq │ └── yeast.nc.6.freq ├── create-priors │ ├── DNaseHS_gm12878.wig │ ├── Makefile.am │ ├── Makefile.in │ ├── chrX.fa │ ├── priors.dist │ └── priors.wig ├── draw-mhmm │ ├── Makefile.am │ ├── Makefile.in │ ├── README │ ├── crp0.complete.fim.gvz │ ├── crp0.complete.gvz │ ├── crp0.complete.spacer.gvz │ ├── crp0.linear.fim.gvz │ ├── crp0.linear.gvz │ ├── crp0.linear.spacer.gvz │ ├── crp0.star.gvz │ ├── crp0.star.spacer.gvz │ ├── lipo.complete.fim.gvz │ ├── lipo.complete.gvz │ ├── lipo.complete.spacer.gvz │ ├── lipo.linear.fim.gvz │ ├── lipo.linear.gvz │ ├── lipo.linear.spacer.gvz │ ├── lipo.star.gvz │ └── lipo.star.spacer.gvz ├── dreme │ ├── Makefile.am │ ├── Makefile.in │ ├── basic.xml │ └── norc.xml ├── fasta-center │ ├── Makefile.am │ ├── Makefile.in │ ├── README │ └── mid3.fasta ├── fimo │ ├── GCN4.meme.txt │ ├── GCN4_YPD-genomic.fasta │ ├── GCN4_YPD-genomic.psp │ ├── GCN4_YPD.fasta │ ├── GCN4_YPD.psp │ ├── MCM1.meme.html │ ├── Makefile.am │ ├── Makefile.in │ ├── fimo-motif23.txt │ ├── fimo-motif23.xml │ ├── fimo-priors-genomic.txt │ ├── fimo-priors.txt │ ├── fimo.txt │ ├── fimo.xml │ ├── prior.dist.txt │ └── spiked.fasta ├── glam2 │ ├── Makefile.am │ ├── Makefile.in │ └── glam2.txt ├── glam2scan │ ├── Makefile.am │ ├── Makefile.in │ └── glam2scan.txt ├── gomo │ ├── GO2Gene.map.csv │ ├── Makefile.am │ ├── Makefile.in │ ├── ama.nozscoring.xml │ ├── ama.redundant.xml │ ├── ama.withMaxodds.xml │ ├── ama.zscoring.xml │ ├── gomo.multipeSpecies.txt │ ├── gomo.smallthreshold.txt │ ├── motif.meme.txt │ ├── seqs.bg │ ├── seqs.fasta │ ├── seqs.norc.bg │ └── seqs_red.fasta ├── mast │ ├── Makefile.am │ ├── Makefile.in │ ├── mast.INO_up800.oops │ ├── mast.INO_up800.tcm │ ├── mast.INO_up800.zoops │ ├── mast.adh.oops │ ├── mast.adh.oops.mini-drosoph │ ├── mast.adh.tcm │ ├── mast.adh.tcm.mini-drosoph │ ├── mast.adh.zoops │ ├── mast.adh.zoops.mini-drosoph │ ├── mast.crp0.oops │ ├── mast.crp0.tcm │ ├── mast.crp0.zoops │ ├── mast.farntrans5.oops │ ├── mast.farntrans5.tcm │ ├── mast.farntrans5.zoops │ ├── mast.lipocalin.oops │ ├── mast.lipocalin.tcm │ └── mast.lipocalin.zoops ├── mcast │ ├── Makefile.am │ ├── Makefile.in │ ├── lex0.zoops.cisml │ ├── lex0.zoops.gff │ ├── lex0.zoops.html │ ├── lex0.zoops.txt │ └── lex0.zoops.xml ├── meme-chip │ ├── JASPAR_CORE_2014_vertebrates.meme │ ├── Klf1.100.s │ ├── Makefile.am │ ├── Makefile.in │ ├── combined.meme │ ├── meme-chip.html │ └── summary.tsv ├── meme │ ├── Makefile.am │ ├── Makefile.in │ ├── meme.INO_up800.oops.html │ ├── meme.INO_up800.oops.txt │ ├── meme.INO_up800.oops.xml │ ├── meme.INO_up800.tcm.html │ ├── meme.INO_up800.tcm.txt │ ├── meme.INO_up800.tcm.xml │ ├── meme.INO_up800.zoops.html │ ├── meme.INO_up800.zoops.txt │ ├── meme.INO_up800.zoops.xml │ ├── meme.adh.oops.html │ ├── meme.adh.oops.txt │ ├── meme.adh.oops.xml │ ├── meme.adh.tcm.html │ ├── meme.adh.tcm.txt │ ├── meme.adh.tcm.xml │ ├── meme.adh.zoops.html │ ├── meme.adh.zoops.txt │ ├── meme.adh.zoops.xml │ ├── meme.crp0.oops.html │ ├── meme.crp0.oops.txt │ ├── meme.crp0.oops.xml │ ├── meme.crp0.tcm.html │ ├── meme.crp0.tcm.txt │ ├── meme.crp0.tcm.xml │ ├── meme.crp0.zoops.html │ ├── meme.crp0.zoops.txt │ ├── meme.crp0.zoops.xml │ ├── meme.farntrans5.oops.html │ ├── meme.farntrans5.oops.txt │ ├── meme.farntrans5.oops.xml │ ├── meme.farntrans5.tcm.html │ ├── meme.farntrans5.tcm.txt │ ├── meme.farntrans5.tcm.xml │ ├── meme.farntrans5.zoops.html │ ├── meme.farntrans5.zoops.txt │ ├── meme.farntrans5.zoops.xml │ ├── meme.lex0.zoops.txt │ ├── meme.lipocalin.oops.html │ ├── meme.lipocalin.oops.txt │ ├── meme.lipocalin.tcm.html │ ├── meme.lipocalin.tcm.txt │ ├── meme.lipocalin.tcm.xml │ ├── meme.lipocalin.zoops.html │ ├── meme.lipocalin.zoops.txt │ ├── meme.lipocalin.zoops.xml │ └── meme.psp_test.zoops ├── mhmm │ ├── Makefile.am │ ├── Makefile.in │ ├── README │ ├── crp0.complete.fim.mhmm │ ├── crp0.complete.mhmm │ ├── crp0.complete.spacer.mhmm │ ├── crp0.linear.fim.mhmm │ ├── crp0.linear.mhmm │ ├── crp0.linear.spacer.mhmm │ ├── crp0.star.mhmm │ ├── crp0.star.spacer.mhmm │ ├── lipo.complete.fim.mhmm │ ├── lipo.complete.mhmm │ ├── lipo.complete.spacer.mhmm │ ├── lipo.linear.fim.mhmm │ ├── lipo.linear.mhmm │ ├── lipo.linear.spacer.mhmm │ ├── lipo.star.mhmm │ └── lipo.star.spacer.mhmm ├── mhmms │ ├── Makefile.am │ ├── Makefile.in │ ├── crp0.complete.all.mhmms │ ├── crp0.complete.fim.all.mhmms │ ├── crp0.complete.fim.single.mhmms │ ├── crp0.complete.single.mhmms │ ├── crp0.complete.spacer.all.mhmms │ ├── crp0.complete.spacer.single.mhmms │ ├── crp0.linear.all.mhmms │ ├── crp0.linear.fim.all.mhmms │ ├── crp0.linear.fim.single.mhmms │ ├── crp0.linear.single.mhmms │ ├── crp0.linear.spacer.all.mhmms │ ├── crp0.linear.spacer.single.mhmms │ ├── crp0.star.all.mhmms │ ├── crp0.star.single.mhmms │ ├── crp0.star.spacer.all.mhmms │ ├── crp0.star.spacer.single.mhmms │ ├── lipo.complete.all.mhmms │ ├── lipo.complete.fim.all.mhmms │ ├── lipo.complete.fim.single.mhmms │ ├── lipo.complete.single.mhmms │ ├── lipo.complete.spacer.all.mhmms │ ├── lipo.complete.spacer.single.mhmms │ ├── lipo.linear.all.mhmms │ ├── lipo.linear.fim.all.mhmms │ ├── lipo.linear.fim.single.mhmms │ ├── lipo.linear.single.mhmms │ ├── lipo.linear.spacer.all.mhmms │ ├── lipo.linear.spacer.single.mhmms │ ├── lipo.star.all.mhmms │ ├── lipo.star.single.mhmms │ ├── lipo.star.spacer.all.mhmms │ ├── lipo.star.spacer.single.mhmms │ ├── r1584.fasta │ ├── r1584.hmm │ ├── r1584.mhmms │ ├── r1635.fasta │ ├── r1635.global.mhmms │ ├── r1635.maxseqs.mhmms │ └── r1635.mhmms ├── mhmmscan │ ├── Makefile.am │ ├── Makefile.in │ └── mhmmscan.txt ├── momo │ ├── Makefile.am │ ├── Makefile.in │ ├── default-comet-no-fasta.txt │ ├── default-msgf-no-fasta.txt │ ├── default-no-fasta.txt │ ├── default-with-fasta-no-mass-in-motif-names.txt │ ├── default-with-fasta.txt │ ├── elim0.txt │ ├── elim3.txt │ ├── filterxcorrrankle3.txt │ ├── modl-default.txt │ ├── mtfx-s0.05-c1-no-mass-in-motif-names-bg-kmers-only-bgfreqs.txt │ ├── mtfx-s0.05-c1-no-mass-in-motif-names.txt │ ├── mtfx-s0.05-c1-smpmT.txt │ ├── mtfx-s0.05-c1.txt │ ├── single-motif-per-mass.txt │ ├── small-comet-mod.txt │ ├── small-msgf-mod.txt │ ├── small-tide-mod-1-out-of-2.txt │ ├── small-tide-mod-2-out-of-2.txt │ ├── small-tide-mod-phospho.fasta │ ├── small-tide-mod-phospho.txt │ ├── small-tide-mod.txt │ ├── small-yeast-prealigned-no-unknowns.txt │ └── small-yeast.fasta ├── motiph │ ├── MCM1.meme.html │ ├── Makefile.am │ ├── Makefile.in │ ├── motiph-motif23.gff │ ├── motiph.gff │ ├── shadow.gff │ ├── spiked.aln │ ├── spiked.fasta │ └── yeast.tree ├── psp-gen │ ├── Makefile.am │ ├── Makefile.in │ ├── README │ ├── all-A.fasta │ ├── one-peak-dna-revcomp.psp │ ├── one-peak-dna.fasta │ ├── one-peak-protein.fasta │ └── one-peak-protein.psp ├── qvalue │ ├── Makefile.am │ ├── Makefile.in │ ├── null.txt │ ├── observed.out │ ├── observed.txt │ ├── uniform.out │ └── uniform.txt ├── scaffold │ ├── Makefile.am │ ├── Makefile.in │ ├── crp0.fasta │ ├── crp0.meme-io │ ├── crp0.prior │ ├── lipo.fasta │ ├── lipo.meme-io │ └── lipo.prior ├── scripts │ ├── Makefile.am │ ├── Makefile.in │ ├── ama.test │ ├── ame.test │ ├── centrimo.test │ ├── clustalw2fasta.test │ ├── create_priors.test │ ├── dreme.test │ ├── fasta-center.test │ ├── fasta-dinucleotide-shuffle.test │ ├── fasta-io.test │ ├── fimo.test │ ├── glam2.test │ ├── glam2scan.test │ ├── gomo.test │ ├── mast.test │ ├── mcast.test │ ├── meme-chip.test │ ├── meme.test │ ├── mhmm-io.test │ ├── mhmm_core.test │ ├── mhmms.test │ ├── mhmmscan.test │ ├── momo.test │ ├── motif-in.test │ ├── motiph.test │ ├── pspgen.test │ ├── qvalue.test │ ├── shadow.test │ ├── spamo.test │ ├── test_driver.pl.in │ └── tomtom.test ├── spamo │ ├── Makefile.am │ ├── Makefile.in │ ├── limits.fasta │ ├── limits.html │ ├── primary.meme │ ├── random.fasta │ ├── random.html │ └── secondary.meme ├── tomtom │ ├── Makefile.am │ ├── Makefile.in │ ├── tomtom.complete.out.allr │ ├── tomtom.complete.out.blic1 │ ├── tomtom.complete.out.blic5 │ ├── tomtom.complete.out.ed │ ├── tomtom.complete.out.kullback │ ├── tomtom.complete.out.pearson │ ├── tomtom.complete.out.sandelin │ ├── tomtom.out.allr │ ├── tomtom.out.blic1 │ ├── tomtom.out.blic5 │ ├── tomtom.out.ed │ ├── tomtom.out.kullback │ ├── tomtom.out.pearson │ └── tomtom.out.sandelin └── web │ ├── Makefile.am │ └── Makefile.in ├── website.mk └── website ├── alternate └── doc │ └── js │ └── menu-path.js ├── canvas-test.html ├── css ├── component_bfile.css ├── component_glam2motifs.css ├── component_motifs.css ├── component_sequences.css ├── fasta-debug.css ├── show_sequence_dbs.css ├── status.css └── tomtom.css ├── images ├── euclidean-eq.png ├── logo_alignment.png ├── pearson-eq.png └── sandelin-eq.png ├── index.html ├── js ├── alphabet_parser.js ├── ame.js ├── bg_parser.js ├── centrimo.js ├── component_bfile.js ├── component_glam2motifs.js ├── component_motifs.js ├── component_sequences.js ├── dreme.js ├── fasta-debug.js ├── fimo.js ├── glam2.js ├── glam2scan.js ├── gomo.js ├── mast.js ├── mcast.js ├── meme-chip.js ├── meme.js ├── menu-path.js ├── momo.js ├── motif_parser.js ├── selectdb.js ├── show_sequence_dbs.js ├── site.js ├── spamo.js ├── status.js └── tomtom.js ├── lib ├── JSAP-2.1.jar ├── JSAP.LICENSE ├── axis.LICENSE ├── axis.jar ├── cog-axis.jar ├── cog-jglobus.jar ├── cog.LICENSE ├── commons-discovery-0.5.jar ├── commons-discovery.LICENSE ├── commons-discovery.NOTICE ├── commons-io-2.4.jar ├── commons-io.LICENSE ├── commons-io.NOTICE ├── commons-logging-1.1.3.jar ├── commons-logging.LICENSE ├── commons-logging.NOTICE ├── commons-net-3.3.jar ├── commons-net.LICENSE ├── commons-net.NOTICE ├── javamail-1.4.3.jar ├── jaxrpc.jar ├── jsoup-1.7.3.jar ├── jsoup.LICENSE ├── jtar-1.1.jar ├── jtar.LICENSE ├── opal-ws-2.5.jar ├── sqlite-jdbc-3.7.2.jar ├── sqlite-jdbc.LICENSE ├── wsdl4j-1.6.3.jar └── wsdl4j.LICENSE ├── src └── au │ └── edu │ └── uq │ └── imb │ └── memesuite │ ├── data │ ├── Alph.java │ ├── AlphStd.java │ ├── AlphType.java │ ├── AlphabetDataSource.java │ ├── Background.java │ ├── MemeSuiteProperties.java │ ├── MotifDataSource.java │ ├── MotifInfo.java │ ├── MotifStats.java │ ├── NamedFileDataSource.java │ ├── PsmDataSource.java │ ├── SequenceDataSource.java │ ├── SequenceInfo.java │ └── SequenceStats.java │ ├── db │ ├── Category.java │ ├── DBList.java │ ├── GomoDB.java │ ├── GomoDBList.java │ ├── GomoDBSecondary.java │ ├── Listing.java │ ├── MotifDB.java │ ├── MotifDBFile.java │ ├── MotifDBList.java │ ├── SQL.java │ ├── SequenceDB.java │ ├── SequenceDBList.java │ ├── SequencePrior.java │ └── SequenceVersion.java │ ├── io │ ├── alph │ │ └── AlphParser.java │ ├── fasta │ │ ├── FastaException.java │ │ ├── FastaHandler.java │ │ ├── FastaParseException.java │ │ ├── FastaParser.java │ │ └── FastaWriter.java │ ├── html │ │ ├── HDataEvent.java │ │ ├── HDataEventType.java │ │ ├── HDataHandler.java │ │ ├── HDataHandlerAdapter.java │ │ ├── HDataParseException.java │ │ ├── HDataParser.java │ │ └── HDataPullParser.java │ └── json │ │ ├── JsonHandler.java │ │ ├── JsonHandlerAdapter.java │ │ ├── JsonParser.java │ │ ├── JsonToken.java │ │ └── JsonType.java │ ├── servlet │ ├── Ame.java │ ├── Centrimo.java │ ├── ConfigurationLoader.java │ ├── Dreme.java │ ├── EchoFile.java │ ├── Fimo.java │ ├── Glam2.java │ ├── Glam2Request.java │ ├── Glam2scan.java │ ├── Gomo.java │ ├── JobStatus.java │ ├── LogoRequest.java │ ├── Mast.java │ ├── Mcast.java │ ├── Meme.java │ ├── MemeRequest.java │ ├── Memechip.java │ ├── Momo.java │ ├── PermanentRedirect.java │ ├── ShowGomoDBs.java │ ├── ShowMotifDBs.java │ ├── ShowSequenceDBs.java │ ├── Spamo.java │ ├── SubmitJob.java │ ├── Tomtom.java │ ├── TomtomRequest.java │ └── util │ │ ├── ComponentAdvancedOptions.java │ │ ├── ComponentBfile.java │ │ ├── ComponentFooter.java │ │ ├── ComponentGlam2Motifs.java │ │ ├── ComponentGomo.java │ │ ├── ComponentHeader.java │ │ ├── ComponentJobDetails.java │ │ ├── ComponentMotifs.java │ │ ├── ComponentSequenceAlphabet.java │ │ ├── ComponentSequences.java │ │ ├── ComponentSubmitReset.java │ │ ├── FeedbackFastaWriter.java │ │ ├── FeedbackHandler.java │ │ ├── Glam2Validator.java │ │ ├── MotifValidator.java │ │ ├── PageComponent.java │ │ ├── StreamCopier.java │ │ └── WebUtils.java │ ├── template │ ├── HTMLSub.java │ ├── HTMLSubGenerator.java │ ├── HTMLTemplate.java │ └── HTMLTemplateCache.java │ ├── updatedb │ ├── AbstractFtpSource.java │ ├── EPDUpdater.java │ ├── EPDUpdater.properties │ ├── EnsemblBacteriaUpdater.java │ ├── EnsemblBacteriaUpdater.properties │ ├── EnsemblFungiUpdater.java │ ├── EnsemblFungiUpdater.properties │ ├── EnsemblMetazoaUpdater.java │ ├── EnsemblMetazoaUpdater.properties │ ├── EnsemblPlantsUpdater.java │ ├── EnsemblPlantsUpdater.properties │ ├── EnsemblProtistsUpdater.java │ ├── EnsemblProtistsUpdater.properties │ ├── EnsemblUpdater.java │ ├── EnsemblUpdater.properties │ ├── FtpFileListUpdater.java │ ├── FtpFileListUpdater.properties │ ├── FtpSource.java │ ├── GenbankUpdater.java │ ├── GenbankUpdater.properties │ ├── PatternFileFilter.java │ ├── RsatUpdater.java │ ├── RsatUpdater.properties │ ├── SequenceProcessor.java │ ├── SequenceUpdater.java │ ├── Source.java │ ├── UCSCGenomeUpdater.java │ ├── UCSCGenomeUpdater.properties │ ├── UpdateSequenceDB.java │ └── UpdateSequenceDB.properties │ └── util │ ├── BMString.java │ ├── FileCoord.java │ ├── GlobFilter.java │ ├── JsonWr.java │ ├── MultiSourceStatus.java │ ├── Progress.java │ ├── SampleStats.java │ └── SemanticVersion.java ├── templates ├── ame.tmpl ├── ame_verify.tmpl ├── centrimo.tmpl ├── centrimo_verify.tmpl ├── component_adv_btn.tmpl ├── component_bfile.tmpl ├── component_footer.tmpl ├── component_glam2motifs.tmpl ├── component_gomo.tmpl ├── component_header.tmpl ├── component_job_details.tmpl ├── component_motifs.tmpl ├── component_sequences.tmpl ├── component_submit_reset.tmpl ├── dreme.tmpl ├── dreme_verify.tmpl ├── email.tmpl ├── fimo.tmpl ├── fimo_verify.tmpl ├── glam2.tmpl ├── glam2_verify.tmpl ├── glam2scan.tmpl ├── glam2scan_verify.tmpl ├── gomo.tmpl ├── gomo_verify.tmpl ├── mast.tmpl ├── mast_verify.tmpl ├── mcast.tmpl ├── mcast_verify.tmpl ├── meme-chip.tmpl ├── meme-chip_verify.tmpl ├── meme.tmpl ├── meme_verify.tmpl ├── momo.tmpl ├── momo_verify.tmpl ├── request_redirect.tmpl ├── show_gomo_dbs.tmpl ├── show_motif_dbs.tmpl ├── show_sequence_dbs.tmpl ├── spamo.tmpl ├── spamo_verify.tmpl ├── status.tmpl ├── tomtom.tmpl ├── tomtom_verify.tmpl ├── verify.tmpl └── whine.tmpl └── web.xml /ARCHIVE_DATE: -------------------------------------------------------------------------------- 1 | Tue Jun 27 16:22:50 2017 -0700 2 | -------------------------------------------------------------------------------- /ARCHIVE_REVISION: -------------------------------------------------------------------------------- 1 | aacc9c3eb8c7b460b344d5c8aa1458097dae704d 2 | 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