Biological Software: Nucleic acid secondary structure.



infernal
description Inference of RNA secondary structure alignments "covariance models" (CMs)
version 1.0.2
homepage http://infernal.janelia.org/
commands cmalign cmbuild cmcalibrate cmemit cmscore cmsearch cmstat
manpages
documentation http://bioweb2.pasteur.fr/docs/infernal/Userguide.pdf
interfaces

mfold
description RNA and DNA secondary structure prediction using nearest neighbor thermodynamic rules.
version 3.2
homepage http://www.bioinfo.rpi.edu/applications/mfold/
commands mfold
manpages
documentation http://bioweb2.pasteur.fr/docs/mfold/
interfaces mfold

unafold
description RNA and DNA secondary structure prediction
version 3.8
homepage http://mfold.rna.albany.edu/?q=DINAMelt/software
commands ITC-plot.pl ct2rnaml hybrid-min hybrid2-min.pl UNAFold.pl dG2Cp hybrid-plot-ng hybrid2-x.pl concentration dG2dH hybrid-select.pl hybrid2.pl concentration-same dG2dS hybrid-ss melt.pl concentrations-same.pl ensemble-dg hybrid-ss-2s.pl plot2ann.pl concentrations.pl ensemble-dg-same hybrid-ss-min sbs ct-energy ensemble-ext hybrid-ss-noml ss-count.pl ct-energy-det.pl ensemble-ext-same hybrid-ss-simple vantHoff-plot.pl ct-ext h-num.pl hybrid2-2s-x.pl ct-prob hybrid hybrid2-2s.pl ct-uniq hybrid-2s.pl hybrid2-min-x.pl
manpages ITC-plot.pl.1 ct2rnaml.1 hybrid-min.1 hybrid2-min.pl.1 UNAFold.pl.1 dG2Cp.1 hybrid-plot-ng.1 hybrid2-x.pl.1 concentration.1 dG2dH.1 hybrid-select.pl.1 hybrid2.pl.1 concentration-same.1 dG2dS.1 hybrid-ss.1 melt.pl.1 concentrations-same.pl.1 ensemble-dg.1 hybrid-ss-2s.pl.1 plot2ann.pl.1 concentrations.pl.1 ensemble-dg-same.1 hybrid-ss-min.1 ct-energy.1 ensemble-ext.1 hybrid-ss-noml.1 ss-count.pl ct-energy-det.pl.1 ensemble-ext-same.1 hybrid-ss-simple.1 vantHoff-plot.pl.1 ct-ext.1 h-num.pl.1 hybrid2-2s-x.pl.1 ct-prob.1 hybrid.1 hybrid2-2s.pl ct-uniq.1 hybrid-2s.pl.1 hybrid2-min-x.pl.1
documentation
interfaces

ViennaRNA
description RNA Secondary Structure Prediction and Comparison.
version 1.8.4
homepage http://www.tbi.univie.ac.at/RNA/
commands RNAaliduplex RNAalifold RNAcofold RNAdistance RNAduplex RNAeval RNAfold RNAforester RNAheat RNAinverse RNALfold RNApaln RNApdist RNAplfold RNAplot RNAsubopt RNAup AnalyseDists AnalyseSeqs Kinfold
manpages RNALfold RNAalifold RNAcofold RNAdistance RNAduplex RNAeval RNAfold RNAheat RNAinverse RNApdist RNAplfold RNAplot RNAsubopt RNAup RNAaliduplex AnalyseDists AnalyseSeqs RNAforester Kinfold
documentation
interfaces rnaalifold rnacofold rnadistance rnaduplex rnaeval rnafold rnaheat rnainverse rnalfold rnapdist rnaplfold rnasubopt


Last update: February, 9 2012