Original software Current software Package Resource Input sequence Output Webserver Standalone doi PMID Total citing articles Citing virology articles
mfold mfold UNAFold The RNA Institute one secondary structure http://unafold.rna.albany.edu/ http://unafold.rna.albany.edu/ 10.1126/science.2468181 2468181 6148 1014
mfold UNAFold UNAFold The RNA Institute one secondary structure http://unafold.rna.albany.edu/ http://unafold.rna.albany.edu/ 10.1007/978-1-60327-429-6_1 18712296
CARNA CARNA Freiburg RNA tools Bioinformatics Group Freiburg multiple secondary structure http://rna.informatik.uni-freiburg.de/CARNA/ http://www.bioinf.uni-freiburg.de/Software/ 10.1093/nar/gks491 22689637 8 1
MARNA LocaRNA-P Freiburg RNA tools Bioinformatics Group Freiburg multiple secondary structure http://rna.informatik.uni-freiburg.de/LocARNA/ http://www.bioinf.uni-freiburg.de/Software/ 10.1261/rna.029041.111 22450757 56 7
MARNA LocaRNA Freiburg RNA tools Bioinformatics Group Freiburg multiple secondary structure http://rna.informatik.uni-freiburg.de/LocARNA/ http://www.bioinf.uni-freiburg.de/Software/ 10.1371/journal.pcbi.0030065 17432929 158 2
MARNA MARNA Freiburg RNA tools Bioinformatics Group Freiburg multiple secondary structure http://rna.informatik.uni-freiburg.de/MARNA/ http://www.bioinf.uni-freiburg.de/Software/ 10.1093/bioinformatics/bti550 15972285 69 0
LocalFold LocalFold Bioinformatics Group Freiburg one secondary structure http://www.bioinf.uni-freiburg.de/Software/LocalFold/ 10.1093/nar/gks181 22373926 39 2
GraphClust GraphClust Bioinformatics Group Freiburg multiple secondary structure http://www.bioinf.uni-freiburg.de/Software/GraphClust/ 10.1093/bioinformatics/bts224 22689765 15 0
RNAscClust RNAscClust Bioinformatics Group Freiburg;RTH multiple secondary structure http://www.bioinf.uni-freiburg.de/Software/RNAscClust/ 10.1093/bioinformatics/btx114 28334186 0 0
IPknot IPknot Rtools ncrna.org one pseudoknot secondary structure https://github.com/satoken/ipknot 10.1093/bioinformatics/btr215 21685106 28 2
DAFS DAFS ncrna.org multiple secondary structure https://github.com/satoken/dafs 10.1093/bioinformatics/bts612 23060618 7 1
SCARNA_LM SCARNA_LM ncrna.org multiple multiple sequence alignment 10.1093/bioinformatics/btp261 19376823 6 0
SCARNA MXSCARNA ncrna.org multiple secondary structure https://www.ncrna.org/softwares/mxscarna/dl/ 10.1186/1471-2105-9-33 18215258 44 0
SCARNA SCARNA ncrna.org two secondary structure 10.1093/bioinformatics/btl177 16690634 20 1
Murlet Murlet ncrna.org multiple secondary structure https://www.ncrna.org/softwares/murlet/ 10.1093/bioinformatics/btm146 17459961 37 0
CentroidHomfold CentroidHomfold-LAST Rtools ncrna.org one secondary structure http://rtools.cbrc.jp/ 10.1093/nar/gkr290 21565800 10 0
CentroidFold CentroidFold Rtools ncrna.org one secondary structure http://rtools.cbrc.jp/ https://github.com/satoken/centroid-rna-package 10.1093/bioinformatics/btn601 19095700 81 4
CentroidHomfold CentroidHomfold Rtools ncrna.org one secondary structure http://rtools.cbrc.jp/ 10.1093/bioinformatics/btp228 19478007 16 2
Raccess Raccess Rtools ncrna.org one secondary structure profile http://rtools.cbrc.jp/ 10.1093/bioinformatics/btr276 21531769 14 0
Rchange Rchange Rtools ncrna.org one secondary structure profile http://rtools.cbrc.jp/ 10.1093/bioinformatics/bts097 22373787 7 0
RintD RintD Rtools ncrna.org one secondary structure http://rtools.cbrc.jp/ 10.1186/1471-2164-15-S10-S6 25560710 1 0
CapR CapR Rtools ncrna.org one secondary structure profile http://rtools.cbrc.jp/ https://github.com/fukunagatsu/CapR 10.1186/gb-2014-15-1-r16 24447569 10 0
RIblast RIblast Faculty of Science and Engineering, Waseda University multiple-to-multiple RNA-RNA interaction sites https://github.com/fukunagatsu/RIblast 10.1093/bioinformatics/btx287 28459942 0 0
PHMMTS PSTAG ncrna.org one pseudoknot secondary structure http://pstag.dna.bio.keio.ac.jp/download.html 10.1093/bioinformatics/bti385 15784748 26 0
PHMMTS PHMMTS ncrna.org one pseudoknot secondary structure http://phmmts.dna.bio.keio.ac.jp/download.html 10.1093/bioinformatics/btg1032 12855464 8 0
Rfold Rfold ncrna.org one secondary structure https://www.ncrna.org/softwares/rfold/ 10.1093/bioinformatics/btm591 18056736 17 0
RactIP RactIP ncrna.org one-to-one RNA-RNA interaction sites https://github.com/satoken/ractip 10.1093/bioinformatics/btq372 20823308 21 0
KnotInFrame KnotInFrame RNA shapes studio Bielefeld BioInformatics Service multiple ribosomal -1 frameshift sites with a pseudoknot secondary structure https://bibiserv2.cebitec.uni-bielefeld.de/knotinframe https://bibiserv2.cebitec.uni-bielefeld.de/knotinframe 10.1093/nar/gkn578 18820303 25 12
pAliKiss pAliKiss RNA shapes studio Bielefeld BioInformatics Service multiple pseudoknot secondary structure https://bibiserv2.cebitec.uni-bielefeld.de/palikiss https://bibiserv2.cebitec.uni-bielefeld.de/palikiss 10.1093/bioinformatics/btu649 25273103 10 3
PknotsRG pKiss RNA shapes studio Bielefeld BioInformatics Service one pseudoknot secondary structure https://bibiserv2.cebitec.uni-bielefeld.de/pkiss https://bibiserv2.cebitec.uni-bielefeld.de/pkiss 10.1007/978-3-642-15294-8_5
PknotsRG PknotsRG RNA shapes studio Bielefeld BioInformatics Service one pseudoknot secondary structure 10.1093/nar/gkm258 17478505 63 34
RapidShapes RapidShapes RNA shapes studio Bielefeld BioInformatics Service one secondary structure https://bibiserv2.cebitec.uni-bielefeld.de/rapidshapes https://bibiserv2.cebitec.uni-bielefeld.de/rapidshapes 10.1093/bioinformatics/btq014 20080511 8 0
RNAalishapes RNAalishapes RNA shapes studio Bielefeld BioInformatics Service multiple secondary structure https://bibiserv2.cebitec.uni-bielefeld.de/rnaalishapes https://bibiserv2.cebitec.uni-bielefeld.de/rnaalishapes 10.1093/nar/gkl692 17020924 8 0
RNAcast RNAshapes RNA shapes studio Bielefeld BioInformatics Service one secondary structure https://bibiserv2.cebitec.uni-bielefeld.de/rnashapes https://bibiserv2.cebitec.uni-bielefeld.de/rnashapes 10.1093/bioinformatics/btk010 16357029 134 1
RNAcast RNAcast RNA shapes studio Bielefeld BioInformatics Service multiple secondary structure 10.1093/bioinformatics/bti577 16020472 45 0
GUUGle GUUGle Bielefeld BioInformatics Service one-to-multiple RNA-RNA interaction sites https://bibiserv2.cebitec.uni-bielefeld.de/guugle https://bibiserv2.cebitec.uni-bielefeld.de/guugle 10.1093/bioinformatics/btk041 16403789 12 1
planACstar planACstar Bielefeld BioInformatics Service multiple secondary structure https://bibiserv2.cebitec.uni-bielefeld.de/planACstar 10.1186/1471-2105-11-222 20433706 4 0
RNAhybrid RNAhybrid Bielefeld BioInformatics Service one-to-one RNA-RNA interaction sites https://bibiserv2.cebitec.uni-bielefeld.de/rnahybrid https://bibiserv2.cebitec.uni-bielefeld.de/rnahybrid 10.1261/rna.5248604 15383676 855 84
Foldalign/FoldalignM Foldalign/FoldalignM Center for non-coding RNA in Technology and Health multiple secondary structure http://rth.dk/resources/foldalign http://rth.dk/resources/foldalign 10.1371/journal.pcbi.0030193 17937495 46 2
PETcofold PETcofold Center for non-coding RNA in Technology and Health multiple-to-multiple RNA-RNA interaction sites http://rth.dk/resources/petfold/ http://rth.dk/resources/petfold/ 10.1093/bioinformatics/btq634 21088024 21 1
PETfold PETfold Center for non-coding RNA in Technology and Health multiple secondary structure http://rth.dk/resources/petfold/ http://rth.dk/resources/petfold/ 10.1093/nar/gkn544 18836192 28 2
RIsearch RIsearch Center for non-coding RNA in Technology and Health multiple-to-multiple RNA-RNA interaction sites http://rth.dk/resources/risearch/ 10.1093/bioinformatics/bts519 22923300 17 1
Context Fold Context Fold Michal Ziv-Ukelson's Research Group one secondary structure https://www.cs.bgu.ac.il/~negevcb/contextfold/ 10.1089/cmb.2011.0184 22035327 12 1
microRNA Bi-Targeting microRNA Bi-Targeting Michal Ziv-Ukelson's Research Group multiple-to-multiple RNA-RNA interaction sites https://www.cs.bgu.ac.il/~vaksler/BiTargeting.htm 10.1186/1471-2105-11-249 20465802 9 0
CDS-plotcon CDS-plotcon Brown Lab multiple conserved elements http://guinevere.otago.ac.nz/aef/MLRGD/index.html http://guinevere.otago.ac.nz/aef/MLRGD/software.html 10.1093/bioinformatics/bti007 15347574 28 20
CDS-plotcon SynPlot2 Firth Lab multiple conserved elements http://guinevere.otago.ac.nz/cgi-bin/aef/synplot.pl http://www.firthLab.path.cam.ac.uk/index.html 10.1093/nar/gku981 25326325 14 10
FRESCo FRESCo Broad Institute multiple conserved elements https://www.broadinstitute.org/fresco/fresco 10.1186/s13059-015-0603-7 25853568 2 1
SiPhy SiPhy Broad Institute multiple conserved elements http://portals.broadinstitute.org/genome_bio/siphy/index.html 10.1093/bioinformatics/btp190 19478016 61 0
GERP GERP Sidow Lab multiple conserved elements http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html 10.1101/gr.3577405 15965027 439 1
phastCons phastCons CSHL multiple conserved elements http://compgen.cshl.edu/phast/ 10.1101/gr.3715005 16024819 1401 5
phyloP phyloP CSHL multiple conserved elements http://compgen.cshl.edu/phast/index.php 10.1101/gr.097857.109 19858363 440 1
SCONE SCONE Sunyaev Lab multiple conserved elements http://genetics.bwh.harvard.edu/scone/ 10.1371/journal.pcbi.0030254 18166073 32 0
Dynalign Dynalign RNAstructure Mathews Lab two secondary structure http://rna.urmc.rochester.edu/RNAstructureWeb/index.html http://rna.urmc.rochester.edu/RNAstructure.html 10.1006/jmbi.2001.5351 11902836 163 5
Dynalign Multilign RNAstructure Mathews Lab multiple secondary structure http://rna.urmc.rochester.edu/RNAstructureWeb/index.html http://rna.urmc.rochester.edu/RNAstructure.html 10.1093/bioinformatics/btq726 21193521 10 3
bifold bifold RNAstructure Mathews Lab two RNA-RNA interaction sites http://rna.urmc.rochester.edu/RNAstructureWeb/index.html http://rna.urmc.rochester.edu/RNAstructure.html 10.1017/S1355838299991148 10580474 133 11
DuplexFold DuplexFold RNAstructure Mathews Lab two RNA-RNA interaction sites http://rna.urmc.rochester.edu/RNAstructureWeb/index.html http://rna.urmc.rochester.edu/RNAstructure.html 10.1261/rna.7650904 15272118 124 2
PARTS PARTS RNAstructure Mathews Lab two secondary structure http://rna.urmc.rochester.edu/RNAstructureWeb/index.html http://rna.urmc.rochester.edu/RNAstructure.html 10.1093/nar/gkn043 18304945 19 0
TurboFold TurboKnot RNAstructure Mathews Lab multiple pseudoknot secondary structure http://rna.urmc.rochester.edu/RNAstructureWeb/index.html http://rna.urmc.rochester.edu/RNAstructure.html 10.1093/bioinformatics/bts044 22285566 5 0
TurboFold TurboFold RNAstructure Mathews Lab multiple secondary structure http://rna.urmc.rochester.edu/RNAstructureWeb/index.html http://rna.urmc.rochester.edu/RNAstructure.html 10.1186/1471-2105-12-108 21507242 26 3
Fold Fold RNAstructure Mathews Lab one secondary structure http://rna.urmc.rochester.edu/RNAstructureWeb/index.html http://rna.urmc.rochester.edu/RNAstructure.html 10.1073/pnas.0401799101 15123812 619 77
ProbKnot ProbKnot RNAstructure Mathews Lab one secondary structure http://rna.urmc.rochester.edu/RNAstructureWeb/index.html http://rna.urmc.rochester.edu/RNAstructure.html 10.1261/rna.2125310 20699301 32 2
KNetFold KNetFold Shapiro Group multiple secondary structure https://knetfold.ncifcrf.gov/ https://knetfold.ncifcrf.gov/ 10.1261/rna.2164906 16495232 31 1
CyloFold CyloFold Shapiro Group one pseudoknot secondary structure https://cylofold.ncifcrf.gov 10.1093/nar/gkq432 20501603 15 0
CovaRNA CovaRNA Shapiro Group multiple Long-range nucleotide-covariation https://binkley2.ncifcrf.gov/users/bshapiro//software.html 10.1261/rna.037630.112 23887147 1 0
MPGAfold MPGAfold Shapiro Group multiple secondary structure https://binkley2.ncifcrf.gov/users/bshapiro//software.html 10.1007/978-1-4939-0348-1_13 24696339 0 0
Srna Srna Sfold Ding RNA Bioinformatics Lab one secondary structure http://sfold.wadsworth.org/cgi-bin/index.pl http://sfold.wadsworth.org/cgi-bin/index.pl 10.1093/nar/gkg938 14654704 204 4
Crumple Crumple Schroeder lab one secondary structure http://adenosine.chem.ou.edu/software.html 10.1016/j.bpj.2011.05.053 21723827 26 0
Sliding Windows and Assembly Sliding Windows and Assembly Schroeder lab one secondary structure http://adenosine.chem.ou.edu/software.html 10.1016/j.bpj.2011.05.053 21723827
Helix Find and Combine Helix Find and Combine Schroeder lab one pseudoknot secondary structure http://adenosine.chem.ou.edu/software.html 10.1016/j.bpj.2011.05.053 21723827
R-scape R-scape Eddy/Rivas Lab multiple secondary structure http://eddylab.org/R-scape/ http://eddylab.org/R-scape/ 10.1038/nmeth.4066 27819659 3 0
TORNADO TORNADO Eddy/Rivas Lab one secondary structure http://eddylab.org/software.html 10.1261/rna.030049.111 22194308 22 0
QRNA QRNA Eddy/Rivas Lab two ncRNA gene prediction http://eddylab.org/software.html 10.1186/1471-2105-2-8 11801179
Pknots Pknots Eddy/Rivas Lab one pseudoknot secondary structure http://eddylab.org/software.html 10.1006/jmbi.1998.2436 9925784 294 11
MultiRNAFold MultiRNAFold RNAsoft Bioinformatics, Empirical and Theoretical Algorithmics (BETA) Lab multiple secondary structure http://www.rnasoft.ca/download.html 10.1016/j.jmb.2004.10.082 15644199 62 0
PairFold PairFold RNAsoft Bioinformatics, Empirical and Theoretical Algorithmics (BETA) Lab one-to-one RNA-RNA interaction sites http://www.rnasoft.ca/cgi-bin/RNAsoft/PairFold/pairfold.pl 10.1093/nar/gkg612 12824338 51 0
HotKnots HotKnots RNAsoft Bioinformatics, Empirical and Theoretical Algorithmics (BETA) Lab one pseudoknot secondary structure http://www.rnasoft.ca/cgi-bin/RNAsoft/HotKnots/hotknots.pl 10.1261/rna.7284905 16199760 79 5
GTFold GTFold Discrete Mathematical Biology lab one secondary structure https://github.com/gtfold/gtfold 10.1145/1529282.1529497
CoFold CoFold e-rna.org Meyer Lab one secondary structure http://www.e-rna.org/cofold/ https://github.com/jujubix/cofold 10.1093/nar/gkt174 23511969 7 1
Transat Transat e-rna.org Meyer Lab multiple secondary structure http://www.e-rna.org/transat/ https://github.com/jujubix/transat 20589081 10 2
SimulFold SimulFold e-rna.org Meyer Lab multiple secondary structure http://www.e-rna.org/simulfold/ https://github.com/jujubix/simulfold 10.1371/journal.pcbi.0030149 17696604 28 0
RNA-Decoder RNA-Decoder e-rna.org Meyer Lab multiple secondary structure http://www.e-rna.org/simulfold/ https://github.com/jujubix/rnadecoder 10.1093/nar/gkh839 15448187 40 10
McQFold PhyloQFold Statistical Genetics Group multiple secondary structure http://evol.bio.lmu.de/_statgen/software/phyloqfold/ 10.1093/bioinformatics/bts369 22796961 2 0
McQFold McQFold Statistical Genetics Group one secondary structure http://www-stud.informatik.uni-frankfurt.de/~metzler/McQFold/ 10.1007/s00285-007-0106-6 17589847 24 1
Pfold Pfold Bioinformatics Research Centre (BiRC) multiple secondary structure http://daimi.au.dk/~compbio/pfold/ 10.1093/nar/gkg614 12824339 181 21
Pfold PPfold Bioinformatics Research Centre (BiRC) multiple secondary structure http://daimi.au.dk/~compbio/pfold/downloads.html 10.1186/1471-2105-12-103 21501497 12 0
RNAG RNAG Center for Computational Molecular Biology, Brown University multiple secondary structure http://ccmbweb.ccv.brown.edu/rnag.html 10.1093/bioinformatics/btr421 21788211 6 0
NUPACK NUPACK nupack.org NUPACK Team one secondary structure http://nupack.org http://nupack.org 10.1002/jcc.21596 20645303 191 3
RNAripalign RNAripalign Bioinformatics Leipzig multiple-to-multiple RNA-RNA interaction sites http://www.bioinf.uni-leipzig.de/~qin/software.html 10.1093/bioinformatics/btq659 21134894 13 0
Carnac Carnac Bonsai Bioinformatics two secondary structure http://bioinfo.lifl.fr/RNA/carnac/carnac.php http://bioinfo.lifl.fr/RNA/carnac/carnac.php 10.1093/bioinformatics/19.1.108 12499300 27 0
RAF RAF CONTRA Serafim Lab multiple secondary structure http://contra.stanford.edu/contrafold/raf.html 10.1093/bioinformatics/btn177 18586747 23 0
CONTRAfold CONTRAfold CONTRA Serafim Lab one secondary structure http://contra.stanford.edu/contrafold/ 10.1093/bioinformatics/btl246 16873527 140 5
inteRNA inteRNA taveRNA Lab for Computational Biology one-to-one RNA-RNA interaction sites http://compbio.cs.sfu.ca/nwp-content/software/taverna/interna/ 10.1089/cmb.2006.13.267 16597239 47 0
piRNA piRNA taveRNA Lab for Computational Biology one-to-one RNA-RNA interaction sites http://compbio.cs.sfu.ca/nwp-content/software/taverna/pirna/ 10.1093/bioinformatics/btp212 19478011 23 0
smyRNA smyRNA taveRNA Lab for Computational Biology one ncRNA gene prediction http://compbio.cs.sfu.ca/nwp-content/software/taverna/smyrna/ 10.1371/journal.pone.0005433 19415115 5 0
RAGE RAGE Notredame's Lab multiple multiple sequence alignment http://tcoffee.org/Projects/raga/ 10.1093/nar/25.22.4570 9358168 46 1
R-Coffee R-Coffee T-Coffee Notredame's Lab multiple multiple sequence alignment http://tcoffee.crg.cat/apps/tcoffee/do:rcoffee http://www.tcoffee.org/Projects/tcoffee/index.html 10.1093/nar/gkn278 18483080 24 2
M-Coffee M-Coffee T-Coffee Notredame's Lab multiple multiple sequence alignment http://tcoffee.crg.cat/apps/tcoffee/do:mcoffee http://www.tcoffee.org/Projects/tcoffee/index.html 10.1093/nar/gkl091 16556910 199 7
LARA LARA LiSA tools CWI - Life Sciences group multiple secondary structure http://www.mi.fu-berlin.de/w/LiSA/Lara 10.1186/1471-2105-8-271 17662141 33 1
MASTR MASTR The Bioinformatics Centre (UCPH) multiple secondary structure http://servers.binf.ku.dk/mastr/ 10.1093/bioinformatics/btm525 18006551 26 0
RNASampler RNASampler Storma Lab multiple secondary structure http://stormo.wustl.edu/RNASampler/ 10.1093/bioinformatics/btm272 17537756 33 0
comRNA comRNA Storma Lab multiple secondary structure http://stormo.wustl.edu/comRNA/ 10.1093/bioinformatics/bth131 14962926 47 0
StructRED StructRED Storma Lab one secondary structure http://stormo.wustl.edu/StructRED/ 10.1038/msb.2009.24 19401680 18 0
CMfinder CMfinder Computational and Synthetic Biology Group multiple secondary structure http://bio.cs.washington.edu/yzizhen/CMfinder/ 10.1093/bioinformatics/btk008 16357030 114 0
RaveNnA RaveNnA Computational and Synthetic Biology Group multiple ncRNA gene prediction http://bliss.biology.yale.edu/~zasha/ravenna/ 10.1093/bioinformatics/bth925 15262817 17 0
SPARCS SPARCS Computer Science and Biology (McGill) one secondary structure profile http://csb.cs.mcgill.ca/sparcs/ http://csb.cs.mcgill.ca/sparcs/ 10.1093/nar/gkt461 23748952 3 2
StrAl StrAl Steger Group multiple multiple sequence alignment https://github.com/andreas-wilm/stral 10.1093/bioinformatics/btl142 16613908 31 1
ConStruct ConStruct Steger Group multiple secondary structure https://github.com/andreas-wilm/construct3 10.1093/nar/27.21.4208 10518612 49 11
vsfold/vs_subopt vsfold/vs_subopt The High Technology Research Center (Chiba Institute of Technology) one pseudoknot secondary structure http://www.rna.it-chiba.ac.jp/~vsfold/vsfold5/ 10.1080/15257770500446915 16541960 12 1
Xrate Xrate DART Holmes Lab multiple conserved elements https://github.com/ihh/dart 10.1186/1471-2105-7-428 17018148 27 1
Stemloc Stemloc DART Holmes Lab multiple secondary structure https://github.com/ihh/dart 10.1186/1471-2105-6-73 15790387
Stemloc-AMA Stemloc-AMA DART Holmes Lab multiple multiple sequence alignment https://github.com/ihh/dart 10.1093/bioinformatics/btn495 18796475 18 0
Evol Doer Evol Doer DART Holmes Lab two pairwise alignment https://github.com/ihh/dart 10.1186/1471-2105-5-166 15507142 29 0
KineFold KineFold Isambert Lab one secondary structure http://kinefold.curie.fr/ http://kinefold.curie.fr/ 10.1093/nar/gki447 15980546 72 7
MSARi MSARi Berger Group multiple multiple sequence alignment http://cb.csail.mit.edu/cb/MSARi/ 10.1073/pnas.0404193101 15304649 41 0
ddbRNA ddbRNA di Bernardo Lab multiple covarying sites http://dibernardo.tigem.it/softwares/ddbrna 10.1093/bioinformatics/btg229 12967955 25 0
EvoFold EvoFold UCSC Genome Browser UCSC Genome Browser Project Team multiple secondary structure 10.1371/journal.pcbi.0020033 16628248 211 2
RNAwolf RNAwolf Theoretical Biochemistry Group one secondary structure http://www.tbi.univie.ac.at/software/rnawolf/rnawolf.html 10.1093/bioinformatics/btr220 21685061 8 0
MC-Tools MC-Tools Major Lab multiple secondary structure http://www.major.iric.ca/MC-Pipeline/ http://www.major.iric.ca/MajorLabEn/MC-Tools.html 10.1038/nature06684 18322526 288 25
MC-Tools MC-Fold-DP Theoretical Biochemistry Group one secondary structure http://www.tbi.univie.ac.at/software/rnawolf/rnawolf.html 10.1093/bioinformatics/btr220 21685061 8 0
RNAalifold RNAalifold ViennaRNA Package Theoretical Biochemistry Group multiple secondary structure http://rna.tbi.univie.ac.at/ http://rna.tbi.univie.ac.at/ 10.1016/S0022-2836(02)00308-X 12079347 211 25
RNAalifold Alifoldz ViennaRNA Package Theoretical Biochemistry Group multiple secondary structure http://rna.tbi.univie.ac.at/ 10.1016/j.jmb.2004.07.018 15313604 60 0
RNAaliduplex RNAaliduplex ViennaRNA Package Theoretical Biochemistry Group multiple-to-multiple RNA-RNA interaction sites http://rna.tbi.univie.ac.at/ 10.1186/1748-7188-6-26 22115189 506 33
RNAcofold RNAcofold ViennaRNA Package Theoretical Biochemistry Group one-to-one RNA-RNA interaction sites http://rna.tbi.univie.ac.at/ http://rna.tbi.univie.ac.at/ 10.1186/1748-7188-1-3 16722605 89 4
RNAduplex RNAduplex ViennaRNA Package Theoretical Biochemistry Group one-to-one RNA-RNA interaction sites http://rna.tbi.univie.ac.at/ 10.1186/1748-7188-1-3 16722605
RNAduplex RNAplex ViennaRNA Package Theoretical Biochemistry Group one-to-one RNA-RNA interaction sites http://rna.tbi.univie.ac.at/ 10.1093/bioinformatics/btn193 18434344 69 2
RNAfold RNAfold ViennaRNA Package Theoretical Biochemistry Group one secondary structure http://rna.tbi.univie.ac.at/ http://rna.tbi.univie.ac.at/ 10.1007/BF00818163
RNALalifold RNALalifold ViennaRNA Package Theoretical Biochemistry Group multiple secondary structure http://rna.tbi.univie.ac.at/ 10.1007/978-1-59745-514-5_33 17993696
RNALfold RNALfold ViennaRNA Package Theoretical Biochemistry Group one secondary structure http://rna.tbi.univie.ac.at/ 10.1093/bioinformatics/btg388 14734309 61 0
RNAPKplex RNAPKplex ViennaRNA Package Theoretical Biochemistry Group one pseudoknot secondary structure http://rna.tbi.univie.ac.at/ 10.1186/1748-7188-6-26 22115189
RNAup RNAup ViennaRNA Package Theoretical Biochemistry Group one-to-one RNA-RNA interaction sites http://rna.tbi.univie.ac.at/ http://rna.tbi.univie.ac.at/ 10.1007/978-3-540-70600-7_9
RNAsubopt RNAsubopt ViennaRNA Package Theoretical Biochemistry Group secondary structure http://rna.tbi.univie.ac.at/ 10.1017/S1355838200992161 10744018 137 1
AliDot AliDot Theoretical Biochemistry Group multiple secondary structure profile http://www.tbi.univie.ac.at/RNA/Alidot/ 10.1093/nar/26.16.3825 9685502 73 27
RNAz RNAz Theoretical Biochemistry Group multiple secondary structure http://rna.tbi.univie.ac.at/ https://www.tbi.univie.ac.at/%7Ewash/RNAz/ 10.1073/pnas.0409169102 15665081 302 11
RNAstrand RNAstrand Theoretical Biochemistry Group multiple secondary structure http://rna.tbi.univie.ac.at/ http://www.bioinf.uni-leipzig.de/Software/RNAstrand/ 10.1186/1748-7188-2-6 17540014 9 2
PMcomp/PMmulti PMcomp/PMmulti Theoretical Biochemistry Group multiple secondary structure https://www.tbi.univie.ac.at/RNA/PMcomp/ 10.1093/bioinformatics/bth229 15073017 99 0
RNAlien RNAlien Theoretical Biochemistry Group one secondary structure http://rna.tbi.univie.ac.at/rnalien/ http://rna.tbi.univie.ac.at/rnalien/ 10.1093/nar/gkw558 27330139 2 0
RNAspa RNAspa Unger Group multiple secondary structure https://faculty.biu.ac.il/~unger/RNAspa/ 10.1186/1471-2105-8-366 17908318 4 0
RNAslider RNAslider Unger Group one secondary structure https://rnaslider.sourceforge.io/ 10.1186/1471-2105-10-76 19257906 3 0
LRIscan LRIscan Bioinformatics and High Throughput Analysis Jena multiple Long-range nucleotide-covariation http://www.rna.uni-jena.de/en/supplements/lriscan/ 10.1093/bioinformatics/btw323 27288498 0 2
BEAGLE BEAGLE Centre for Molecular Bioinformatics multiple secondary structure http://beagle.bio.uniroma2.it/ 10.1093/nar/gkv489 25977293 2 0
RNA-TVCurve RNA-TVCurve Intelligence Engineering laboratory multiple secondary structure http://ml.jlu.edu.cn/tvcurve/ 10.1186/s12859-017-1481-7 28109252 0 0
ERA ERA UCF CBB Research Group multiple multiple sequence alignment http://genome.ucf.edu/ERA/ 10.1186/1471-2105-14-269 24011432 6 0
RNAscf RNAscf UCF CBB Research Group multiple secondary structure http://genome.ucf.edu/RNAscf/ 10.1089/cmb.2006.13.283 16597240 13 0
PMFastR PMFastR UCF CBB Research Group multiple multiple sequence alignment https://github.com/danfdeblasio/PMFastR.git 10.1109/TCBB.2011.86 21576754 0 0
RNASLOpt RNASLOpt UCF CBB Research Group one secondary structure http://genome.ucf.edu/RNASLOpt/ 10.1093/bioinformatics/btr510 21903624 5 0
RNASLOpt RNAConSLOpt UCF CBB Research Group multiple secondary structure http://genome.ucf.edu/RNAConSLOpt/ 10.1504/IJBRA.2014.062997 24989865
Riboswitch finder Riboswitch finder Chair of Bioinformatics (phylogenetics) one riboswitch http://riboswitch.bioapps.biozentrum.uni-wuerzburg.de/server.html 10.1093/nar/gkh352 15215370 24 0
RNA Analyzer RNA Analyzer Chair of Bioinformatics (phylogenetics) one secondary structure http://rnaanalyzer.bioapps.biozentrum.uni-wuerzburg.de/ 10.1093/nar/gkg568 12824342 21 0
ParasoR ParasoR Kiryu Laboratory one secondary structure https://github.com/carushi/ParasoR 10.1186/s12859-016-1067-9 27153986 1 0
RNAProfile RNAProfile MoD Tools BeaCon Lab multiple secondary structure http://159.149.160.56/beacon/ 10.1093/nar/gkh650 15199174 31 0
RNApromo RNApromo Segal Lab multiple secondary structure http://genie.weizmann.ac.il/pubs/rnamotifs08/rnamotifs08_predict.html https://genie.weizmann.ac.il/pubs/rnamotifs08/rnamotifs08_exe.html 10.1073/pnas.0803169105 18815376 44 0
RNAbor RNAbor Clote Lab one secondary structure http://bioinformatics.bc.edu/clotelab/RNAbor 10.1093/bioinformatics/btm314 17573364 19 1
RNA-WL RNA-WL Clote Lab one secondary structure https://sourceforge.net/projects/rna-wl/ 10.1093/bioinformatics/btq218 20529917 5 0
RNAbor RNAborMEA Clote Lab one secondary structure http://bioinformatics.bc.edu/clotelab/RNAborMEA/srcCode/index.html 10.1186/1471-2105-13-S5-S6 22537010 8 1
RNAlocopt RNAlocopt Clote Lab one secondary structure http://bioinformatics.bc.edu/clotelab/RNAlocopt http://bioinformatics.bc.edu/clotelab/RNAlocopt 10.1371/journal.pone.0016178 21297972 18 0
KnotSeeker DotKnot Datta Lab one pseudoknot secondary structure http://dotknot.csse.uwa.edu.au/ http://dotknot.csse.uwa.edu.au/ 10.1093/nar/gkq021 20123730 25 14
KnotSeeker DotKnot-PW Datta Lab two pseudoknot secondary structure 10.1093/bioinformatics/bts575 23044552 2 0
KnotSeeker KnotSeeker Datta Lab one pseudoknot secondary structure http://staffhome.ecm.uwa.edu.au/~00033579/pseudoknot/ 10.1261/rna.968808 18314500 17 8
ILM ILM Zhang lab multiple pseudoknot secondary structure http://www.cs.wustl.edu/~zhang/projects/rna/ilm/ 10.1093/bioinformatics/btg373 14693809 81 4
GeneBee GeneBee GeneBee Group multiple secondary structure http://www.genebee.msu.su/services/rna2_reduced.html 7578577
GArna GArna Institute of Cytology and Genetics, SB RAS one secondary structure http://wwwmgs.bionet.nsc.ru/mgs/programs/2dstructrna/ 10.1023/A:1020945806836 5 0
HXMATCH HXMATCH Theoretical Biochemistry Group multiple pseudoknot secondary structure https://www.tbi.univie.ac.at/papers/SUPPLEMENTS/HXMATCH/ 10.1109/TCBB.2004.22 17048382 23 0
Seed Seed Turcotte Lab multiple secondary structure http://bio.site.uottawa.ca/software/seed/ 10.1186/1471-2105-7-244 16677380 3 0
Dynalign X-Dynalign Turcotte Lab three secondary structure http://bio.site.uottawa.ca/software/x-dynalign/ 10.1504/IJBRA.2005.007581 18048133 2 0
Dynalign Profile-Dynalign Turcotte Lab multiple secondary structure http://bio.site.uottawa.ca/software/profile-dynalign/ 10.1186/1471-2105-8-190 17559658 4 0
Riboswitch Scanner Riboswitch Scanner one riboswitch http://service.iiserkol.ac.in/~riboscan/application.html http://service.iiserkol.ac.in/~riboscan/application.html 10.1093/bioinformatics/btv640 1 0
McGenus McGenus International School for Advanced Studies (SISSA) one pseudoknot secondary structure http://eole2.lsce.ipsl.fr/ipht/tt2ne/mcgenus.php 10.1093/nar/gks1204 23248008 12 0
TT2NE TT2NE International School for Advanced Studies (SISSA) one pseudoknot secondary structure http://eole2.lsce.ipsl.fr/ipht/tt2ne/mcgenus.php 10.1093/nar/gkr240 21593129 9 0
Vfold Vfold2D Shi-Jie Chen Research Group one secondary structure http://rna.physics.missouri.edu/index.html http://rna.physics.missouri.edu/src/index.html 10.1371/journal.pone.0107504 25215508 13 0
Vfold VfoldCPX Shi-Jie Chen Research Group one-to-one RNA-RNA structure http://rna.physics.missouri.edu/index.html http://rna.physics.missouri.edu/src/index.html 10.1371/journal.pone.0163454 27657918 0 0
P-DCFold P-DCFold EvryRNA AROBAS Team multiple pseudoknot secondary structure https://evryrna.ibisc.univ-evry.fr/evryrna/ https://evryrna.ibisc.univ-evry.fr/evryrna/ 10.1142/S021821300500234X 2 0
BiokoP BiokoP EvryRNA AROBAS Team pseudoknot secondary structure https://evryrna.ibisc.univ-evry.fr/evryrna/
SSCA SSCA EvryRNA AROBAS Team multiple secondary structure https://evryrna.ibisc.univ-evry.fr/evryrna/ https://evryrna.ibisc.univ-evry.fr/evryrna/ 10.1186/1471-2105-8-464 18045491 5 0
SSCA Tfold EvryRNA AROBAS Team multiple secondary structure https://evryrna.ibisc.univ-evry.fr/evryrna/ https://evryrna.ibisc.univ-evry.fr/evryrna/ 10.1093/nar/gkp1067 20047957 8 0
Cofolga Cofolga Akito Taneda Lab two secondary structure 10.1016/j.compbiolchem.2005.02.004 15833439 3 1
Cofolga Cofolga2mo Akito Taneda Lab multiple secondary structure http://rna.eit.hirosaki-u.ac.jp/cofolga2mo/ 10.1093/bioinformatics/btq439 20679330 14 0
RNA-Pareto RNA-Pareto Bioinformatics & Systems Biology, Universität Ulm multiple multiple sequence alignment http://sysbio.uni-ulm.de/soft/RNA-Pareto/ 10.1093/bioinformatics/btt536 24045774 2 0
PicXAA PicXAA-R Yoon Lab multiple multiple sequence alignment http://www.ece.tamu.edu/~bjyoon/picxaa/ 10.1186/1471-2105-12-S1-S38 21342569 8 0
PicXAA PicXAA Yoon Lab multiple multiple sequence alignment http://www.ece.tamu.edu/~bjyoon/picxaa/ 10.1093/nar/gkq255 20413579 20 0
SSE SSE Simmonds Lab variety toolkit http://www.virus-evolution.org/Downloads/Software/ 10.1186/1756-0500-5-50 22264264 78 76