Break RNA Pseudoknots
This item, unique to RNA, breaks pseudoknots in an RNA secondary structure, leaving a pseudoknot-free structure. See "Break RNA Pseudoknots."

Dot Plot
This item allows the display of a dot plot using one of many save file types generated from various manipulations of a sequence. See "Dot Plot."

Draw
This item will draw any structure saved in the CT file format. See "Draw."

Dynalign
This item opens the Dynalign tool, which will find the sequence alignment and the lowest free energy common structure common to two sequences. See "Dynalign."

Efn2
This item will determine the free energy of a secondary structure saved in the CT file format. See "Efn2."

Fold Single Strand
This item will open a folding window. This is the traditional structure prediction algorithm that finds lowest free energy structures. See "Fold."

Fold Bimolecular
This item will predict the intermolecular secondary structures of two oligonucleotides. See "Fold -> Bimolecular Folding."

Generate All Suboptimal Structures
This item allows the prediction of all possible secondary structures within a specified energy increment of the lowest free energy structure. See "Generate All Suboptimal Structures."

MaxExpect: Predict MEA Structure
This item predicts maximum expected accuracy structures, which are structures composed of the most probable pairs. See "Maximum Expected Accuracy."

Multilign
This item predicts common secondary structures for multiple sequences (more than two). See "Multilign."

OligoScreen
This item opens the OligoScreen tool, which determines thermodynamic parameters for a set of oligonucleotides. See "OligoScreen."

OligoWalk
This item opens the OligoWalk tool, which can help to determine an oligomer that will hybridize tightly to a target. See "OligoWalk."

Partition Function
This item uses a partition function calculation to predict base pair probabilities for any canonical pair in the sequence. See "Partition Function."

Partition Function Bimolecular
This item uses a partition function calculation to predict base pair probabilities for base pairs between two sequences. See "Partition Function -> Bimolecular Partitioning."

ProbKnot: Predict Structures Including Pseudoknots
This item will predict a maximum expected accuracy structure, including pseudoknots, from a partition function save file, and save the result as a CT file. See "ProbKnot."

Refold
This item can be used to predict a different set of suboptimal secondary structures from a previously folded sequence or calculation. See "Refold."

Stochastic Sampling
This item generates a sample of secondary structures for a sequence, drawn from the complete folding ensemble. See "Stochastic Sampling."

TurboFold
This item predicts common secondary structures for multiple sequences (more than two) using base pairing probabilities. See "TurboFold."