├── .DS_Store ├── .project ├── .pydevproject ├── 3rdParty ├── .DS_Store ├── transterm │ ├── 2ndscore.cc │ ├── LICENSE.txt │ ├── Makefile │ ├── RELEASE-NOTES.txt │ ├── USAGE.txt │ ├── analysis.cc │ ├── analysis.h │ ├── analysis.o │ ├── anti.cc │ ├── anti.o │ ├── calibrate.sh │ ├── conf.cc │ ├── conf.h │ ├── conf.o │ ├── distr.cc │ ├── distr.h │ ├── distr.o │ ├── ermolaeva-oldconf.cc │ ├── ermolaeva-oldconf.o │ ├── ermolaeva-score.cc │ ├── ermolaeva-score.h │ ├── ermolaeva-score.o │ ├── expterm.dat │ ├── fake.coords │ ├── gen.fa │ ├── gene-reader.cc │ ├── gene-reader.h │ ├── gene-reader.o │ ├── make_expterm.py │ ├── map-output.cc │ ├── map-output.h │ ├── map-output.o │ ├── mfold_rna.sh │ ├── random_fasta.py │ ├── search.cc │ ├── search.h │ ├── search.o │ ├── seq.cc │ ├── seq.h │ ├── seq.o │ ├── test-fake.coords │ ├── test.fa │ ├── transterm │ ├── transterm.cc │ ├── transterm.h │ ├── transterm.o │ ├── util.cc │ ├── util.h │ └── util.o ├── unafold │ ├── .DS_Store │ ├── ITC-plot.pl │ ├── ITC-plot.pl.in │ ├── Makefile │ ├── Makefile.am │ ├── Makefile.in │ ├── UNAFold.pl │ ├── UNAFold.pl.in │ ├── concentrations-same.pl │ ├── concentrations-same.pl.in │ ├── concentrations.pl │ ├── concentrations.pl.in │ ├── ct-energy │ ├── ct-energy-det.pl │ ├── ct-energy-det.pl.in │ ├── ct2rnaml │ ├── data │ │ ├── .DS_Store │ │ ├── Makefile │ │ ├── Makefile.am │ │ ├── Makefile.in │ │ ├── asint1x2.DAT │ │ ├── asint1x2.DG │ │ ├── asint1x2.DGD │ │ ├── asint1x2.DH │ │ ├── asint1x2.DHD │ │ ├── asint1x2.NUL │ │ ├── asint1x2.NULD │ │ ├── asint1x2.NULDAT │ │ ├── dangle.DAT │ │ ├── dangle.DG │ │ ├── dangle.DGD │ │ ├── dangle.DH │ │ ├── dangle.DHD │ │ ├── dangle.NUL │ │ ├── dangle.NULD │ │ ├── dangle.NULDAT │ │ ├── extinction.DAT │ │ ├── hexaloop.DAT │ │ ├── hexaloop.DG │ │ ├── hexaloop.DGD │ │ ├── hexaloop.DH │ │ ├── hexaloop.DHD │ │ ├── hexaloop.NUL │ │ ├── hexaloop.NULD │ │ ├── hexaloop.NULDAT │ │ ├── loop.DAT │ │ ├── loop.DG │ │ ├── loop.DGD │ │ ├── loop.DH │ │ ├── loop.DHD │ │ ├── loop.NUL │ │ ├── loop.NULD │ │ ├── loop.NULDAT │ │ ├── miscloop.DAT │ │ ├── miscloop.DG │ │ ├── miscloop.DGD │ │ ├── miscloop.DH │ │ ├── miscloop.DHD │ │ ├── miscloop.NUL │ │ ├── miscloop.NULD │ │ ├── miscloop.NULDAT │ │ ├── rules │ │ │ ├── asint1x2.dat │ │ │ ├── asint1x2.dg │ │ │ ├── asint1x2.dgd │ │ │ ├── asint1x2.dh │ │ │ ├── asint1x2.dhd │ │ │ ├── coaxial.dat │ │ │ ├── coaxstack.dat │ │ │ ├── dangle.dat │ │ │ ├── dangle.dg │ │ │ ├── dangle.dgd │ │ │ ├── dangle.dh │ │ │ ├── dangle.dhd │ │ │ ├── extinction.dat │ │ │ ├── extinction.dat.bp │ │ │ ├── hexaloop.dat │ │ │ ├── hexaloop.dg │ │ │ ├── hexaloop.dgd │ │ │ ├── hexaloop.dh │ │ │ ├── hexaloop.dhd │ │ │ ├── loop.dat │ │ │ ├── loop.dg │ │ │ ├── loop.dgd │ │ │ ├── loop.dh │ │ │ ├── loop.dhd │ │ │ ├── miscloop.dat │ │ │ ├── miscloop.dg │ │ │ ├── miscloop.dgd │ │ │ ├── miscloop.dh │ │ │ ├── miscloop.dhd │ │ │ ├── sint2.dat │ │ │ ├── sint2.dg │ │ │ ├── sint2.dgd │ │ │ ├── sint2.dh │ │ │ ├── sint2.dhd │ │ │ ├── sint4.dat │ │ │ ├── sint4.dg │ │ │ ├── sint4.dgd │ │ │ ├── sint4.dh │ │ │ ├── sint4.dhd │ │ │ ├── stack.dat │ │ │ ├── stack.dg │ │ │ ├── stack.dgd │ │ │ ├── stack.dh │ │ │ ├── stack.dhd │ │ │ ├── tloop.dat │ │ │ ├── tloop.dg │ │ │ ├── tloop.dgd │ │ │ ├── tloop.dh │ │ │ ├── tloop.dhd │ │ │ ├── triloop.dat │ │ │ ├── triloop.dg │ │ │ ├── triloop.dgd │ │ │ ├── triloop.dh │ │ │ ├── triloop.dhd │ │ │ ├── tstackcoax.dat │ │ │ ├── tstacke.dat │ │ │ ├── tstacke.dg │ │ │ ├── tstacke.dgd │ │ │ ├── tstacke.dh │ │ │ ├── tstacke.dhd │ │ │ ├── tstackh.dat │ │ │ ├── tstackh.dg │ │ │ ├── tstackh.dgd │ │ │ ├── tstackh.dh │ │ │ ├── tstackh.dhd │ │ │ ├── tstacki.dat │ │ │ ├── tstacki.dg │ │ │ ├── tstacki.dgd │ │ │ ├── tstacki.dh │ │ │ ├── tstacki.dhd │ │ │ ├── tstackm.dat │ │ │ ├── tstackm.dg │ │ │ ├── tstackm.dgd │ │ │ ├── tstackm.dh │ │ │ └── tstackm.dhd │ │ ├── sint2.DAT │ │ ├── sint2.DG │ │ ├── sint2.DGD │ │ ├── sint2.DH │ │ ├── sint2.DHD │ │ ├── sint2.NUL │ │ ├── sint2.NULD │ │ ├── sint2.NULDAT │ │ ├── sint4.DAT │ │ ├── sint4.DG │ │ ├── sint4.DGD │ │ ├── sint4.DH │ │ ├── sint4.DHD │ │ ├── sint4.NUL │ │ ├── sint4.NULD │ │ ├── sint4.NULDAT │ │ ├── stack.DAT │ │ ├── stack.DG │ │ ├── stack.DGD │ │ ├── stack.DH │ │ ├── stack.DHD │ │ ├── stack.NUL │ │ ├── stack.NULD │ │ ├── stack.NULDAT │ │ ├── tloop.DAT │ │ ├── tloop.DG │ │ ├── tloop.DGD │ │ ├── tloop.DH │ │ ├── tloop.DHD │ │ ├── tloop.NUL │ │ ├── tloop.NULD │ │ ├── tloop.NULDAT │ │ ├── triloop.DAT │ │ ├── triloop.DG │ │ ├── triloop.DGD │ │ ├── triloop.DH │ │ ├── triloop.DHD │ │ ├── triloop.NUL │ │ ├── triloop.NULD │ │ ├── triloop.NULDAT │ │ ├── tstacke.DAT │ │ ├── tstacke.DG │ │ ├── tstacke.DGD │ │ ├── tstacke.DH │ │ ├── tstacke.DHD │ │ ├── tstacke.NUL │ │ ├── tstacke.NULD │ │ ├── tstacke.NULDAT │ │ ├── tstackh.DAT │ │ ├── tstackh.DG │ │ ├── tstackh.DGD │ │ ├── tstackh.DH │ │ ├── tstackh.DHD │ │ ├── tstackh.NUL │ │ ├── tstackh.NULD │ │ ├── tstackh.NULDAT │ │ ├── tstacki.DAT │ │ ├── tstacki.DG │ │ ├── tstacki.DGD │ │ ├── tstacki.DH │ │ ├── tstacki.DHD │ │ ├── tstacki.NUL │ │ ├── tstacki.NULD │ │ ├── tstacki.NULDAT │ │ ├── tstackm.DAT │ │ ├── tstackm.DG │ │ ├── tstackm.DGD │ │ ├── tstackm.DH │ │ ├── tstackm.DHD │ │ ├── tstackm.NUL │ │ ├── tstackm.NULD │ │ └── tstackm.NULDAT │ ├── h-num.pl │ ├── h-num.pl.in │ ├── hybrid-2s.pl │ ├── hybrid-2s.pl.in │ ├── hybrid-min │ ├── hybrid-select.pl │ ├── hybrid-select.pl.in │ ├── hybrid-ss-2s.pl │ ├── hybrid-ss-2s.pl.in │ ├── hybrid-ss-min │ ├── hybrid2.pl │ ├── hybrid2.pl.in │ ├── melt.pl │ ├── melt.pl.in │ ├── plot2ann.pl │ ├── plot2ann.pl.in │ ├── ss-count.pl │ ├── ss-count.pl.in │ ├── vantHoff-plot.pl │ └── vantHoff-plot.pl.in └── vienna │ ├── RNAeval │ ├── RNAplfold │ └── RNAsubopt ├── DBOperation ├── DBAbstract.py ├── DBAbstract.pyc ├── DBSQLite.py ├── DBSQLite.pyc ├── __init__.py └── __init__.pyc ├── Data.py ├── Data.pyc ├── DesignOfExperiments ├── Design.py ├── Design.pyc ├── __init__.py └── __init__.pyc ├── Features ├── .DS_Store ├── Bottleneck.py ├── Bottleneck.pyc ├── CAI.py ├── CAI.pyc ├── Feature.py ├── Feature.pyc ├── HydropathyIndex.py ├── HydropathyIndex.pyc ├── Motif.py ├── Motif.pyc ├── NucleotideContent.py ├── NucleotideContent.pyc ├── RNADuplex.py ├── RNADuplex.pyc ├── Structure.py ├── Structure.pyc ├── StructureEnsemble.py ├── StructureEnsemble.pyc ├── StructureProb.py ├── StructureProb.pyc ├── __init__.py └── __init__.pyc ├── Functions.py ├── Functions.pyc ├── LICENSE ├── README ├── RunningExamples ├── .DS_Store ├── Analyzer │ ├── .DS_Store │ ├── TIPEcoli.py │ ├── TranslationFeaturesEcoliAnalyzer.py │ ├── TranslationFeaturesEcoliAnalyzer.pyc │ ├── __init__.py │ └── __init__.pyc ├── Designer │ ├── .DS_Store │ ├── BacterialPromotersDesigner.py │ ├── BacterialPromotersDesigner.pyc │ ├── TIPDesigner.py │ ├── TranslationFeaturesEcoliDesigner.py │ ├── TranslationFeaturesEcoliDesigner.pyc │ ├── __init__.py │ └── __init__.pyc ├── __init__.py └── __init__.pyc ├── SequenceAnalyzer.py ├── SequenceAnalyzer.pyc ├── SequenceDesigner.py ├── SequenceDesigner.pyc ├── Solution.py ├── Solution.pyc ├── Utils ├── ComputeMinimalSet.py ├── ComputeMinimalSet.pyc ├── DB2CSV.py ├── DB2CSV.pyc ├── DB2FASTA.py ├── DB2FASTA.pyc ├── DBKinetics.py ├── DBKinetics.pyc ├── DBStatistics.py ├── DBStatistics.pyc ├── __init__.py ├── __init__.pyc ├── pfm2pwm.py ├── pfm2pwm.pyc ├── pwmScoresSample.py └── pwmScoresSample.pyc ├── __init__.py ├── db └── .DS_Store ├── testFiles ├── .DS_Store ├── auxiliaryData │ ├── .DS_Store │ ├── TIP_seed_sequences.csv │ ├── random_60nt.csv │ └── taniguchi_pa_dataset.csv ├── genomes │ ├── ecoli_genome.csv │ └── partial_ecoli_genome.csv ├── outputFiles │ └── .DS_Store └── pwm │ ├── .DS_Store │ └── e.coli │ ├── .DS_Store │ ├── operators │ ├── .DS_Store │ └── ecoli_lacI.pwm │ ├── promoters │ ├── ecoli_s70_10.pwm │ ├── ecoli_s70_35.pwm │ ├── ecoli_s70_sp15.pwm │ ├── ecoli_s70_sp16.pwm │ ├── ecoli_s70_sp17.pwm │ ├── ecoli_s70_sp18.pwm │ └── ecoli_s70_sp19.pwm │ └── sd │ └── ecoli_sd.pwm ├── tmp ├── .DS_Store └── cleanFolders.sh └── tutorial └── 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