|   | NUCLEIC 2D STRUCTURE | 
Nucleic acid secondary structure
| Program name | Description | 
|---|---|
| einverted | Finds inverted repeats in nucleotide sequences | 
| vrnaalifold | RNA alignment folding | 
| vrnaalifoldpf | RNA alignment folding with partition | 
| vrnacofold | RNA cofolding | 
| vrnacofoldconc | RNA cofolding with concentrations | 
| vrnacofoldpf | RNA cofolding with partitioning | 
| vrnadistance | RNA distances | 
| vrnaduplex | RNA duplex calculation | 
| vrnaeval | RNA eval | 
| vrnaevalpair | RNA eval with cofold | 
| vrnafold | Calculate secondary structures of RNAs | 
| vrnafoldpf | Secondary structures of RNAs with partition | 
| vrnaheat | RNA melting | 
| vrnainverse | RNA sequences matching a structure | 
| vrnalfold | Calculate locally stable secondary structures of RNAs | 
| vrnaplot | Plot vrnafold output | 
| vrnasubopt | Calculate RNA suboptimals |