| Program name | Description | 
|---|
| ovrnaalifold | Calculate secondary structures for a set of aligned RNAs | 
| ovrnaalifoldpf | Calculate secondary structures for a set of aligned RNAs (partition) | 
| ovrnacofold | Calculate secondary structures of RNA dimers | 
| ovrnacofoldconc | Calculate secondary structures of RNA dimers (concentrations) | 
| ovrnacofoldpf | Calculate secondary structures of RNA dimers (partitioning) | 
| ovrnadistance | Calculate distances between RNA secondary structures | 
| ovrnaduplex | Predict RNA duplex (hybridization) sites and structure | 
| ovrnaeval | Calculate energy of RNA sequences with a given secondary structure | 
| ovrnaevalpair | Calculate energy of RNA sequences on given secondary structure | 
| ovrnafold | Calculate min. energy RNA structure / pair probabilities (partition) | 
| ovrnafoldpf | Calculate min. energy RNA structure / pair probabilities | 
| ovrnaheat | Calculate specific heat of RNA melting | 
| ovrnainverse | Find RNA sequences with a given secondary structure | 
| ovrnalfold | Calculate locally stable secondary structures of RNAs | 
| ovrnaplot | Draw RNA secondary structures | 
| ovrnasubopt | Calculate suboptimal secondary structure of RNA | 
| vrna2dfold | Calculate RNA structures and samples of k,l neighbourhoods | 
| vrnaaliduplex | RNA duplex calculation for two sequence alignments | 
| vrnaalifold | Calculate secondary structures for a set of aligned RNAs | 
| vrnaalifoldpf | Calculate secondary structures for a set of aligned RNAs (partition) | 
| vrnacofold | Calculate secondary structures of RNA dimers | 
| vrnacofoldconc | Calculate secondary structures of RNA dimers (concentrations) | 
| vrnacofoldpf | Calculate secondary structures of RNA dimers (partitioning) | 
| vrnadistance | Calculate distances between RNA secondary structures | 
| vrnaduplex | Predict RNA duplex (hybridization) sites and structure | 
| vrnaeval | Calculate energy of RNA sequences with a given secondary structure | 
| vrnaevalpair | Calculate energy of RNA sequences on given secondary structure | 
| vrnafold | Calculate min. energy RNA secondary structures and pair probabilities | 
| vrnafoldpf | Calculate min. energy RNA structures / pair probabilities (partition) | 
| vrnaheat | Calculate specific heat of RNA melting | 
| vrnainverse | Find RNA sequences with a given secondary structure | 
| vrnalalifoldpf | Calculate secondary structures for a set of aligned RNAs (partition) | 
| vrnalfold | Calculate locally stable secondary structures of RNAs | 
| vrnalfoldz | Calculate locally stable secondary structures of RNAs plus zscore | 
| vrnapkplex | Calculate RNA structures plus pseudoknots | 
| vrnaplfold | Compute avg. pair probabilities for local base pairs in RNA sequences | 
| vrnaplot | Draw RNA secondary structures | 
| vrnasubopt | Calculate suboptimal secondary structures of RNAs |