|
A
AccessFold: Overview
AccessFold: References
AccessFold: Run Information
Alignment File Format
alignments
AllSub: Overview
AllSub: References
AllSub: Run Information |
N
NAPSS: Overview
NAPSS: References
NAPSS: Run Information
NMR Data Integrated With Structure Prediction
|
|
B
bifold: Overview
bifold: References
bifold: Run Information
Bimolecular Folding
Bimolecular Duplex Folding
Bimolecular Duplex Folding with Accessibility
Bimolecular Partition Function
bipartition: Overview
bipartition: References
bipartition: Run Information
Building the Text Interfaces
|
O
Offset File Format
oligoscreen: Overview
oligoscreen: References
oligoscreen: Run Information
OligoWalk
|
|
C
Calculating Ensemble Energy
Calculating Common Structures For Multiple Sequences
Calculating Common Structures For Two Sequences
CircleCompare: Overview
CircleCompare: References
CircleCompare: Run Information
Comparing Two Structures
Converting Bracket Files to CT Files
Converting CT Files to Bracket Files
CT File Format
ct2dot: Overview
ct2dot: References
ct2dot: Run Information
cuda: partition-cuda |
P
partition: Overview
partition: References
partition: Run Information
Partition Function Single Strand
PARTS: Overview
PARTS: References
PARTS: Run Information
pathways for analysis
phmm
Probability of Pairs in Two Unaligned Sequences
ProbabilityPlot: Overview
ProbabilityPlot: References
ProbabilityPlot: Run Information
ProbablePair: Overview
ProbablePair: References
ProbablePair: Run Information
ProbKnot: Overview
ProbKnot: References
ProbKnot: Run Information
ProbScan
Pseudoknot Prediction: ProbKnot
Pseudoknot Prediction: ShapeKnots |
|
D
dot2ct: Overview
dot2ct: References
dot2ct: Run Information
draw: Overview
draw: References
draw: Run Information
Drawing Secondary Structures
Drawing a Base Pairing Probability Dot Plot
Drawing a Dynalign Dot Plot
Drawing a Folding Free Energy Dot Plot
DuplexFold: Overview
DuplexFold: References
DuplexFold: Run Information
dynalign: Overview
dynalign: References
dynalign: Run Information
dynalign-smp: Overview
dynalign-smp: References
dynalign-smp: Run Information
DynalignDotPlot: Overview
DynalignDotPlot: References
DynalignDotPlot: Run Information
|
Q
|
|
E
efn2: Overview
efn2: References
efn2: Run Information
Energy Function 2
EnergyPlot: Overview
EnergyPlot: References
EnergyPlot: Run Information
EnsembleEnergy: Overview
EnsembleEnergy: References
EnsembleEnergy: Run Information
Experimental Pair Bonus File Format
|
R
refold: Overview
refold: References
refold: Run Information
Refolding Previously Folded Structures
RemovePseudoknots: Overview
RemovePseudoknots: References
RemovePseudoknots: Run Information
Removing Pseudoknots
|
|
F
FASTA File Format
File Formats
Folding Free Energy Calculation
Fold: Overview
Fold: References
Fold: Run Information
Fold-cuda
Folding Constraint File Format
Folding Single Stranded Structures
Folding on GPUs |
S
scorer: Overview
scorer: References
scorer: Run Information
Scoring a Structure's Quality
Sequence File Format
SHAPE Restraint File Format
ShapeKnots
Specifying Thermodynamic Parameters
Stochastic Sampling |
|
G
Generating All Suboptimal Structures
Generating Probable Structures
|
T
Thermodynamic Parameters for Oligos
TurboFold: Overview
TurboFold: References
TurboFold: Run Information
|
|
H
|
U
|
|
I
Identifying Pseudoknots
Information flow |
V
|
|
J
|
W
|
|
K
|
X
|
|
L
List File Format
|
Y
|
|
M
MaxExpect: Overview
MaxExpect: References
MaxExpect: Run Information
Maximum Expected Accuracy Structures
Multifind: Overview
Multifind: Run Information
multilign: Overview
multilign: References
multilign: Run Information
multilign-smp: Overview
multilign-smp: References
multilign-smp: Run Information |
Z
|
