# VIENNA Applications

These programs are adapted from the VIENNA RNA package.

This is currently under development, and is available only from the CVS server. We hope to make a beta release in the near future, but there is much work to be done on sequence formats and testing.

### Applications in the current vienna release

Program name | Description
--- | ---
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