\indexentry{RNA Secondary Structure Folding@{RNA Secondary Structure Folding}|hyperpage}{31}
\indexentry{Calculating Minimum Free Energy (MFE) Structures@{Calculating Minimum Free Energy (MFE) Structures}|hyperpage}{33}
\indexentry{mfe\_\discretionary {-}{}{}fold@{mfe\_\discretionary {-}{}{}fold}!fold\_\discretionary {-}{}{}par@{fold\_\discretionary {-}{}{}par}|hyperpage}{34}
\indexentry{fold\_\discretionary {-}{}{}par@{fold\_\discretionary {-}{}{}par}!mfe_fold@{mfe\_\discretionary {-}{}{}fold}|hyperpage}{34}
\indexentry{mfe\_\discretionary {-}{}{}fold@{mfe\_\discretionary {-}{}{}fold}!fold@{fold}|hyperpage}{35}
\indexentry{fold@{fold}!mfe_fold@{mfe\_\discretionary {-}{}{}fold}|hyperpage}{35}
\indexentry{mfe\_\discretionary {-}{}{}fold@{mfe\_\discretionary {-}{}{}fold}!circfold@{circfold}|hyperpage}{35}
\indexentry{circfold@{circfold}!mfe_fold@{mfe\_\discretionary {-}{}{}fold}|hyperpage}{35}
\indexentry{Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{37}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par@{pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}|hyperpage}{39}
\indexentry{pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par@{pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{39}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{39}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{39}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!pf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}|hyperpage}{40}
\indexentry{pf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{40}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!free\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays@{free\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}|hyperpage}{41}
\indexentry{free\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays@{free\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{41}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params@{update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}|hyperpage}{42}
\indexentry{update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params@{update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{42}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!export\_\discretionary {-}{}{}bppm@{export\_\discretionary {-}{}{}bppm}|hyperpage}{42}
\indexentry{export\_\discretionary {-}{}{}bppm@{export\_\discretionary {-}{}{}bppm}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{42}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}pr@{assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}pr}|hyperpage}{42}
\indexentry{assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}pr@{assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}pr}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{42}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!get\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays@{get\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}|hyperpage}{43}
\indexentry{get\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays@{get\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{43}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance@{mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance}|hyperpage}{43}
\indexentry{mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance@{mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{43}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance\_\discretionary {-}{}{}pr@{mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance\_\discretionary {-}{}{}pr}|hyperpage}{43}
\indexentry{mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance\_\discretionary {-}{}{}pr@{mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance\_\discretionary {-}{}{}pr}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{43}
\indexentry{Compute the structure with maximum expected accuracy (MEA)@{Compute the structure with maximum expected accuracy (MEA)}|hyperpage}{45}
\indexentry{Compute the centroid structure@{Compute the centroid structure}|hyperpage}{46}
\indexentry{centroid\_\discretionary {-}{}{}fold@{centroid\_\discretionary {-}{}{}fold}!get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pl@{get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pl}|hyperpage}{46}
\indexentry{get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pl@{get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pl}!centroid_fold@{centroid\_\discretionary {-}{}{}fold}|hyperpage}{46}
\indexentry{centroid\_\discretionary {-}{}{}fold@{centroid\_\discretionary {-}{}{}fold}!get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pr@{get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pr}|hyperpage}{46}
\indexentry{get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pr@{get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pr}!centroid_fold@{centroid\_\discretionary {-}{}{}fold}|hyperpage}{46}
\indexentry{Enumerating Suboptimal Structures@{Enumerating Suboptimal Structures}|hyperpage}{48}
\indexentry{Suboptimal structures according to Zuker et al. 1989@{Suboptimal structures according to Zuker et al. 1989}|hyperpage}{49}
\indexentry{subopt\_\discretionary {-}{}{}zuker@{subopt\_\discretionary {-}{}{}zuker}!zukersubopt@{zukersubopt}|hyperpage}{49}
\indexentry{zukersubopt@{zukersubopt}!subopt_zuker@{subopt\_\discretionary {-}{}{}zuker}|hyperpage}{49}
\indexentry{Suboptimal structures within an energy band arround the MFE@{Suboptimal structures within an energy band arround the MFE}|hyperpage}{50}
\indexentry{subopt\_\discretionary {-}{}{}wuchty@{subopt\_\discretionary {-}{}{}wuchty}!subopt@{subopt}|hyperpage}{50}
\indexentry{subopt@{subopt}!subopt_wuchty@{subopt\_\discretionary {-}{}{}wuchty}|hyperpage}{50}
\indexentry{subopt\_\discretionary {-}{}{}wuchty@{subopt\_\discretionary {-}{}{}wuchty}!subopt\_\discretionary {-}{}{}circ@{subopt\_\discretionary {-}{}{}circ}|hyperpage}{51}
\indexentry{subopt\_\discretionary {-}{}{}circ@{subopt\_\discretionary {-}{}{}circ}!subopt_wuchty@{subopt\_\discretionary {-}{}{}wuchty}|hyperpage}{51}
\indexentry{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}|hyperpage}{52}
\indexentry{subopt\_\discretionary {-}{}{}stochbt@{subopt\_\discretionary {-}{}{}stochbt}!pbacktrack@{pbacktrack}|hyperpage}{52}
\indexentry{pbacktrack@{pbacktrack}!subopt_stochbt@{subopt\_\discretionary {-}{}{}stochbt}|hyperpage}{52}
\indexentry{subopt\_\discretionary {-}{}{}stochbt@{subopt\_\discretionary {-}{}{}stochbt}!pbacktrack\_\discretionary {-}{}{}circ@{pbacktrack\_\discretionary {-}{}{}circ}|hyperpage}{53}
\indexentry{pbacktrack\_\discretionary {-}{}{}circ@{pbacktrack\_\discretionary {-}{}{}circ}!subopt_stochbt@{subopt\_\discretionary {-}{}{}stochbt}|hyperpage}{53}
\indexentry{subopt\_\discretionary {-}{}{}stochbt@{subopt\_\discretionary {-}{}{}stochbt}!st\_\discretionary {-}{}{}back@{st\_\discretionary {-}{}{}back}|hyperpage}{53}
\indexentry{st\_\discretionary {-}{}{}back@{st\_\discretionary {-}{}{}back}!subopt_stochbt@{subopt\_\discretionary {-}{}{}stochbt}|hyperpage}{53}
\indexentry{Calculate Secondary Structures of two RNAs upon Dimerization@{Calculate Secondary Structures of two RNAs upon Dimerization}|hyperpage}{54}
\indexentry{MFE Structures of two hybridized Sequences@{MFE Structures of two hybridized Sequences}|hyperpage}{55}
\indexentry{mfe\_\discretionary {-}{}{}cofold@{mfe\_\discretionary {-}{}{}cofold}!cofold@{cofold}|hyperpage}{55}
\indexentry{cofold@{cofold}!mfe_cofold@{mfe\_\discretionary {-}{}{}cofold}|hyperpage}{55}
\indexentry{mfe\_\discretionary {-}{}{}cofold@{mfe\_\discretionary {-}{}{}cofold}!export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays\_\discretionary {-}{}{}gq@{export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays\_\discretionary {-}{}{}gq}|hyperpage}{56}
\indexentry{export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays\_\discretionary {-}{}{}gq@{export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays\_\discretionary {-}{}{}gq}!mfe_cofold@{mfe\_\discretionary {-}{}{}cofold}|hyperpage}{56}
\indexentry{mfe\_\discretionary {-}{}{}cofold@{mfe\_\discretionary {-}{}{}cofold}!export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays@{export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays}|hyperpage}{56}
\indexentry{export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays@{export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays}!mfe_cofold@{mfe\_\discretionary {-}{}{}cofold}|hyperpage}{56}
\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{58}
\indexentry{pf\_\discretionary {-}{}{}cofold@{pf\_\discretionary {-}{}{}cofold}!co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{59}
\indexentry{co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!pf_cofold@{pf\_\discretionary {-}{}{}cofold}|hyperpage}{59}
\indexentry{pf\_\discretionary {-}{}{}cofold@{pf\_\discretionary {-}{}{}cofold}!co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par@{co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}|hyperpage}{59}
\indexentry{co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par@{co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}!pf_cofold@{pf\_\discretionary {-}{}{}cofold}|hyperpage}{59}
\indexentry{pf\_\discretionary {-}{}{}cofold@{pf\_\discretionary {-}{}{}cofold}!export\_\discretionary {-}{}{}co\_\discretionary {-}{}{}bppm@{export\_\discretionary {-}{}{}co\_\discretionary {-}{}{}bppm}|hyperpage}{60}
\indexentry{export\_\discretionary {-}{}{}co\_\discretionary {-}{}{}bppm@{export\_\discretionary {-}{}{}co\_\discretionary {-}{}{}bppm}!pf_cofold@{pf\_\discretionary {-}{}{}cofold}|hyperpage}{60}
\indexentry{pf\_\discretionary {-}{}{}cofold@{pf\_\discretionary {-}{}{}cofold}!update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params@{update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}|hyperpage}{60}
\indexentry{update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params@{update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}!pf_cofold@{pf\_\discretionary {-}{}{}cofold}|hyperpage}{60}
\indexentry{pf\_\discretionary {-}{}{}cofold@{pf\_\discretionary {-}{}{}cofold}!update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params\_\discretionary {-}{}{}par@{update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params\_\discretionary {-}{}{}par}|hyperpage}{61}
\indexentry{update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params\_\discretionary {-}{}{}par@{update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params\_\discretionary {-}{}{}par}!pf_cofold@{pf\_\discretionary {-}{}{}cofold}|hyperpage}{61}
\indexentry{pf\_\discretionary {-}{}{}cofold@{pf\_\discretionary {-}{}{}cofold}!compute\_\discretionary {-}{}{}probabilities@{compute\_\discretionary {-}{}{}probabilities}|hyperpage}{61}
\indexentry{compute\_\discretionary {-}{}{}probabilities@{compute\_\discretionary {-}{}{}probabilities}!pf_cofold@{pf\_\discretionary {-}{}{}cofold}|hyperpage}{61}
\indexentry{pf\_\discretionary {-}{}{}cofold@{pf\_\discretionary {-}{}{}cofold}!get\_\discretionary {-}{}{}concentrations@{get\_\discretionary {-}{}{}concentrations}|hyperpage}{61}
\indexentry{get\_\discretionary {-}{}{}concentrations@{get\_\discretionary {-}{}{}concentrations}!pf_cofold@{pf\_\discretionary {-}{}{}cofold}|hyperpage}{61}
\indexentry{Partition Function for two hybridized Sequences as a stepwise Process@{Partition Function for two hybridized Sequences as a stepwise Process}|hyperpage}{63}
\indexentry{up\_\discretionary {-}{}{}cofold@{up\_\discretionary {-}{}{}cofold}!pf\_\discretionary {-}{}{}unstru@{pf\_\discretionary {-}{}{}unstru}|hyperpage}{63}
\indexentry{pf\_\discretionary {-}{}{}unstru@{pf\_\discretionary {-}{}{}unstru}!up_cofold@{up\_\discretionary {-}{}{}cofold}|hyperpage}{63}
\indexentry{up\_\discretionary {-}{}{}cofold@{up\_\discretionary {-}{}{}cofold}!pf\_\discretionary {-}{}{}interact@{pf\_\discretionary {-}{}{}interact}|hyperpage}{64}
\indexentry{pf\_\discretionary {-}{}{}interact@{pf\_\discretionary {-}{}{}interact}!up_cofold@{up\_\discretionary {-}{}{}cofold}|hyperpage}{64}
\indexentry{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}|hyperpage}{66}
\indexentry{consensus\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}fold}!get\_\discretionary {-}{}{}mpi@{get\_\discretionary {-}{}{}mpi}|hyperpage}{67}
\indexentry{get\_\discretionary {-}{}{}mpi@{get\_\discretionary {-}{}{}mpi}!consensus_fold@{consensus\_\discretionary {-}{}{}fold}|hyperpage}{67}
\indexentry{consensus\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}fold}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}alistruct@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}alistruct}|hyperpage}{67}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}alistruct@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}alistruct}!consensus_fold@{consensus\_\discretionary {-}{}{}fold}|hyperpage}{67}
\indexentry{consensus\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}fold}!encode\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}sequence@{encode\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}sequence}|hyperpage}{68}
\indexentry{encode\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}sequence@{encode\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}sequence}!consensus_fold@{consensus\_\discretionary {-}{}{}fold}|hyperpage}{68}
\indexentry{consensus\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}fold}!alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays@{alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}|hyperpage}{68}
\indexentry{alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays@{alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}!consensus_fold@{consensus\_\discretionary {-}{}{}fold}|hyperpage}{68}
\indexentry{consensus\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}fold}!free\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays@{free\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}|hyperpage}{69}
\indexentry{free\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays@{free\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}!consensus_fold@{consensus\_\discretionary {-}{}{}fold}|hyperpage}{69}
\indexentry{consensus\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}fold}!get\_\discretionary {-}{}{}alipf\_\discretionary {-}{}{}arrays@{get\_\discretionary {-}{}{}alipf\_\discretionary {-}{}{}arrays}|hyperpage}{69}
\indexentry{get\_\discretionary {-}{}{}alipf\_\discretionary {-}{}{}arrays@{get\_\discretionary {-}{}{}alipf\_\discretionary {-}{}{}arrays}!consensus_fold@{consensus\_\discretionary {-}{}{}fold}|hyperpage}{69}
\indexentry{consensus\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}fold}!cv\_\discretionary {-}{}{}fact@{cv\_\discretionary {-}{}{}fact}|hyperpage}{70}
\indexentry{cv\_\discretionary {-}{}{}fact@{cv\_\discretionary {-}{}{}fact}!consensus_fold@{consensus\_\discretionary {-}{}{}fold}|hyperpage}{70}
\indexentry{consensus\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}fold}!nc\_\discretionary {-}{}{}fact@{nc\_\discretionary {-}{}{}fact}|hyperpage}{70}
\indexentry{nc\_\discretionary {-}{}{}fact@{nc\_\discretionary {-}{}{}fact}!consensus_fold@{consensus\_\discretionary {-}{}{}fold}|hyperpage}{70}
\indexentry{MFE Consensus Structures for Sequence Alignment(s)@{MFE Consensus Structures for Sequence Alignment(s)}|hyperpage}{71}
\indexentry{consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}!alifold@{alifold}|hyperpage}{71}
\indexentry{alifold@{alifold}!consensus_mfe_fold@{consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}|hyperpage}{71}
\indexentry{consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}!circalifold@{circalifold}|hyperpage}{71}
\indexentry{circalifold@{circalifold}!consensus_mfe_fold@{consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}|hyperpage}{71}
\indexentry{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}|hyperpage}{73}
\indexentry{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par@{alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}|hyperpage}{73}
\indexentry{alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par@{alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}!consensus_pf_fold@{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{73}
\indexentry{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!alipf\_\discretionary {-}{}{}fold@{alipf\_\discretionary {-}{}{}fold}|hyperpage}{73}
\indexentry{alipf\_\discretionary {-}{}{}fold@{alipf\_\discretionary {-}{}{}fold}!consensus_pf_fold@{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{73}
\indexentry{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!alipf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold@{alipf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}|hyperpage}{74}
\indexentry{alipf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold@{alipf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}!consensus_pf_fold@{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{74}
\indexentry{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!export\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}bppm@{export\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}bppm}|hyperpage}{74}
\indexentry{export\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}bppm@{export\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}bppm}!consensus_pf_fold@{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{74}
\indexentry{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)@{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}|hyperpage}{75}
\indexentry{consensus\_\discretionary {-}{}{}stochbt@{consensus\_\discretionary {-}{}{}stochbt}!alipbacktrack@{alipbacktrack}|hyperpage}{75}
\indexentry{alipbacktrack@{alipbacktrack}!consensus_stochbt@{consensus\_\discretionary {-}{}{}stochbt}|hyperpage}{75}
\indexentry{Predicting Locally stable structures of large sequences@{Predicting Locally stable structures of large sequences}|hyperpage}{76}
\indexentry{Local MFE structure Prediction and Z-\/scores@{Local MFE structure Prediction and Z-\/scores}|hyperpage}{77}
\indexentry{local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold@{local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}!Lfold@{Lfold}|hyperpage}{77}
\indexentry{Lfold@{Lfold}!local_mfe_fold@{local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}|hyperpage}{77}
\indexentry{local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold@{local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}!Lfoldz@{Lfoldz}|hyperpage}{77}
\indexentry{Lfoldz@{Lfoldz}!local_mfe_fold@{local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}|hyperpage}{77}
\indexentry{Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}|hyperpage}{78}
\indexentry{local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}paramsLP@{update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}paramsLP}|hyperpage}{78}
\indexentry{update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}paramsLP@{update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}paramsLP}!local_pf_fold@{local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{78}
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\indexentry{Local MFE consensus structures for Sequence Alignments@{Local MFE consensus structures for Sequence Alignments}|hyperpage}{81}
\indexentry{local\_\discretionary {-}{}{}consensus\_\discretionary {-}{}{}fold@{local\_\discretionary {-}{}{}consensus\_\discretionary {-}{}{}fold}!aliLfold@{aliLfold}|hyperpage}{81}
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\indexentry{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}|hyperpage}{82}
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\indexentry{Reading/Writing energy parameter sets from/to File@{Reading/Writing energy parameter sets from/to File}|hyperpage}{86}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}rw@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}rw}!read\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file@{read\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}|hyperpage}{86}
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\indexentry{Converting energy parameter files@{Converting energy parameter files}|hyperpage}{88}
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\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}11@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}11}|hyperpage}{90}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}11@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}11}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{90}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}21@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}21}|hyperpage}{90}
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\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}22@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}22}|hyperpage}{90}
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\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}BULGE@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}BULGE}|hyperpage}{90}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}BULGE@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}BULGE}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{90}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT}|hyperpage}{90}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{90}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ML@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ML}|hyperpage}{90}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ML@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ML}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{90}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MISC@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MISC}|hyperpage}{90}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MISC@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MISC}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{90}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}SPECIAL\_\discretionary {-}{}{}HP@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}SPECIAL\_\discretionary {-}{}{}HP}|hyperpage}{90}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}SPECIAL\_\discretionary {-}{}{}HP@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}SPECIAL\_\discretionary {-}{}{}HP}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{90}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}VANILLA@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}VANILLA}|hyperpage}{90}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}VANILLA@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}VANILLA}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{90}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}NINIO@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}NINIO}|hyperpage}{91}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}NINIO@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}NINIO}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{91}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DUMP@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DUMP}|hyperpage}{91}
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\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file@{convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}|hyperpage}{91}
\indexentry{convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file@{convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{91}
\indexentry{Energy evaluation@{Energy evaluation}|hyperpage}{93}
\indexentry{eval@{eval}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure}|hyperpage}{94}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure}!eval@{eval}|hyperpage}{94}
\indexentry{eval@{eval}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}|hyperpage}{94}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}!eval@{eval}|hyperpage}{94}
\indexentry{eval@{eval}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}structure@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}structure}|hyperpage}{94}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}structure@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}structure}!eval@{eval}|hyperpage}{94}
\indexentry{eval@{eval}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}|hyperpage}{95}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}!eval@{eval}|hyperpage}{95}
\indexentry{eval@{eval}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure\_\discretionary {-}{}{}pt@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure\_\discretionary {-}{}{}pt}|hyperpage}{95}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure\_\discretionary {-}{}{}pt@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure\_\discretionary {-}{}{}pt}!eval@{eval}|hyperpage}{95}
\indexentry{eval@{eval}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt\_\discretionary {-}{}{}par@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt\_\discretionary {-}{}{}par}|hyperpage}{96}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt\_\discretionary {-}{}{}par@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt\_\discretionary {-}{}{}par}!eval@{eval}|hyperpage}{96}
\indexentry{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}|hyperpage}{97}
\indexentry{inverse\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}fold}!inverse\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}fold}|hyperpage}{97}
\indexentry{inverse\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}fold}!inverse_fold@{inverse\_\discretionary {-}{}{}fold}|hyperpage}{97}
\indexentry{inverse\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}fold}!inverse\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{98}
\indexentry{inverse\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!inverse_fold@{inverse\_\discretionary {-}{}{}fold}|hyperpage}{98}
\indexentry{inverse\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}fold}!final\_\discretionary {-}{}{}cost@{final\_\discretionary {-}{}{}cost}|hyperpage}{98}
\indexentry{final\_\discretionary {-}{}{}cost@{final\_\discretionary {-}{}{}cost}!inverse_fold@{inverse\_\discretionary {-}{}{}fold}|hyperpage}{98}
\indexentry{inverse\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}fold}!give\_\discretionary {-}{}{}up@{give\_\discretionary {-}{}{}up}|hyperpage}{98}
\indexentry{give\_\discretionary {-}{}{}up@{give\_\discretionary {-}{}{}up}!inverse_fold@{inverse\_\discretionary {-}{}{}fold}|hyperpage}{98}
\indexentry{inverse\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}fold}!inv\_\discretionary {-}{}{}verbose@{inv\_\discretionary {-}{}{}verbose}|hyperpage}{98}
\indexentry{inv\_\discretionary {-}{}{}verbose@{inv\_\discretionary {-}{}{}verbose}!inverse_fold@{inverse\_\discretionary {-}{}{}fold}|hyperpage}{98}
\indexentry{Classified Dynamic Programming@{Classified Dynamic Programming}|hyperpage}{99}
\indexentry{Distance based partitioning of the Secondary Structure Space@{Distance based partitioning of the Secondary Structure Space}|hyperpage}{100}
\indexentry{Calculating MFE representatives of a Distance Based Partitioning@{Calculating MFE representatives of a Distance Based Partitioning}|hyperpage}{101}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}!get\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables@{get\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}|hyperpage}{102}
\indexentry{get\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables@{get\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}!kl_neighborhood_mfe@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}|hyperpage}{102}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}!destroy\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables@{destroy\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}|hyperpage}{102}
\indexentry{destroy\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables@{destroy\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}!kl_neighborhood_mfe@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}|hyperpage}{102}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}!TwoDfoldList@{TwoDfoldList}|hyperpage}{102}
\indexentry{TwoDfoldList@{TwoDfoldList}!kl_neighborhood_mfe@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}|hyperpage}{102}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}!TwoDfold\_\discretionary {-}{}{}backtrack\_\discretionary {-}{}{}f5@{TwoDfold\_\discretionary {-}{}{}backtrack\_\discretionary {-}{}{}f5}|hyperpage}{103}
\indexentry{TwoDfold\_\discretionary {-}{}{}backtrack\_\discretionary {-}{}{}f5@{TwoDfold\_\discretionary {-}{}{}backtrack\_\discretionary {-}{}{}f5}!kl_neighborhood_mfe@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}|hyperpage}{103}
\indexentry{Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}|hyperpage}{104}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}!get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables@{get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}|hyperpage}{105}
\indexentry{get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables@{get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}!kl_neighborhood_pf@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}|hyperpage}{105}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}!get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables\_\discretionary {-}{}{}from\_\discretionary {-}{}{}MFE@{get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables\_\discretionary {-}{}{}from\_\discretionary {-}{}{}MFE}|hyperpage}{105}
\indexentry{get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables\_\discretionary {-}{}{}from\_\discretionary {-}{}{}MFE@{get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables\_\discretionary {-}{}{}from\_\discretionary {-}{}{}MFE}!kl_neighborhood_pf@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}|hyperpage}{105}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}!destroy\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables@{destroy\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}|hyperpage}{105}
\indexentry{destroy\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables@{destroy\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}!kl_neighborhood_pf@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}|hyperpage}{105}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}!TwoDpfoldList@{TwoDpfoldList}|hyperpage}{106}
\indexentry{TwoDpfoldList@{TwoDpfoldList}!kl_neighborhood_pf@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}|hyperpage}{106}
\indexentry{Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}|hyperpage}{107}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt}!TwoDpfold\_\discretionary {-}{}{}pbacktrack@{TwoDpfold\_\discretionary {-}{}{}pbacktrack}|hyperpage}{107}
\indexentry{TwoDpfold\_\discretionary {-}{}{}pbacktrack@{TwoDpfold\_\discretionary {-}{}{}pbacktrack}!kl_neighborhood_stochbt@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt}|hyperpage}{107}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt}!TwoDpfold\_\discretionary {-}{}{}pbacktrack5@{TwoDpfold\_\discretionary {-}{}{}pbacktrack5}|hyperpage}{108}
\indexentry{TwoDpfold\_\discretionary {-}{}{}pbacktrack5@{TwoDpfold\_\discretionary {-}{}{}pbacktrack5}!kl_neighborhood_stochbt@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt}|hyperpage}{108}
\indexentry{Compute the Density of States@{Compute the Density of States}|hyperpage}{109}
\indexentry{dos@{dos}!density\_\discretionary {-}{}{}of\_\discretionary {-}{}{}states@{density\_\discretionary {-}{}{}of\_\discretionary {-}{}{}states}|hyperpage}{109}
\indexentry{density\_\discretionary {-}{}{}of\_\discretionary {-}{}{}states@{density\_\discretionary {-}{}{}of\_\discretionary {-}{}{}states}!dos@{dos}|hyperpage}{109}
\indexentry{Parsing and Comparing -\/ Functions to Manipulate Structures@{Parsing and Comparing -\/ Functions to Manipulate Structures}|hyperpage}{110}
\indexentry{bondT@{bondT}|hyperpage}{111}
\indexentry{bondTEn@{bondTEn}|hyperpage}{112}
\indexentry{cofoldF@{cofoldF}|hyperpage}{113}
\indexentry{ConcEnt@{ConcEnt}|hyperpage}{114}
\indexentry{constrain@{constrain}|hyperpage}{115}
\indexentry{COORDINATE@{COORDINATE}|hyperpage}{116}
\indexentry{cpair@{cpair}|hyperpage}{117}
\indexentry{duplexT@{duplexT}|hyperpage}{118}
\indexentry{dupVar@{dupVar}|hyperpage}{119}
\indexentry{folden@{folden}|hyperpage}{120}
\indexentry{interact@{interact}|hyperpage}{121}
\indexentry{intermediate\_\discretionary {-}{}{}t@{intermediate\_\discretionary {-}{}{}t}|hyperpage}{122}
\indexentry{INTERVAL@{INTERVAL}|hyperpage}{123}
\indexentry{LIST@{LIST}|hyperpage}{124}
\indexentry{LST\_\discretionary {-}{}{}BUCKET@{LST\_\discretionary {-}{}{}BUCKET}|hyperpage}{125}
\indexentry{model\_\discretionary {-}{}{}detailsT@{model\_\discretionary {-}{}{}detailsT}|hyperpage}{126}
\indexentry{model\_\discretionary {-}{}{}detailsT@{model\_\discretionary {-}{}{}detailsT}!dangles@{dangles}|hyperpage}{126}
\indexentry{dangles@{dangles}!model_detailsT@{model\_\discretionary {-}{}{}detailsT}|hyperpage}{126}
\indexentry{move\_\discretionary {-}{}{}t@{move\_\discretionary {-}{}{}t}|hyperpage}{128}
\indexentry{PAIR@{PAIR}|hyperpage}{129}
\indexentry{pair\_\discretionary {-}{}{}info@{pair\_\discretionary {-}{}{}info}|hyperpage}{130}
\indexentry{pairpro@{pairpro}|hyperpage}{131}
\indexentry{paramT@{paramT}|hyperpage}{132}
\indexentry{path\_\discretionary {-}{}{}t@{path\_\discretionary {-}{}{}t}|hyperpage}{133}
\indexentry{pf\_\discretionary {-}{}{}paramT@{pf\_\discretionary {-}{}{}paramT}|hyperpage}{134}
\indexentry{pf\_\discretionary {-}{}{}paramT@{pf\_\discretionary {-}{}{}paramT}!alpha@{alpha}|hyperpage}{134}
\indexentry{alpha@{alpha}!pf_paramT@{pf\_\discretionary {-}{}{}paramT}|hyperpage}{134}
\indexentry{plist@{plist}|hyperpage}{136}
\indexentry{Postorder\_\discretionary {-}{}{}list@{Postorder\_\discretionary {-}{}{}list}|hyperpage}{137}
\indexentry{pu\_\discretionary {-}{}{}contrib@{pu\_\discretionary {-}{}{}contrib}|hyperpage}{138}
\indexentry{pu\_\discretionary {-}{}{}out@{pu\_\discretionary {-}{}{}out}|hyperpage}{139}
\indexentry{sect@{sect}|hyperpage}{140}
\indexentry{snoopT@{snoopT}|hyperpage}{141}
\indexentry{SOLUTION@{SOLUTION}|hyperpage}{142}
\indexentry{struct\_\discretionary {-}{}{}en@{struct\_\discretionary {-}{}{}en}|hyperpage}{143}
\indexentry{svm\_\discretionary {-}{}{}model@{svm\_\discretionary {-}{}{}model}|hyperpage}{144}
\indexentry{swString@{swString}|hyperpage}{145}
\indexentry{Tree@{Tree}|hyperpage}{146}
\indexentry{TwoDfold\_\discretionary {-}{}{}solution@{TwoDfold\_\discretionary {-}{}{}solution}|hyperpage}{147}
\indexentry{TwoDfold\_\discretionary {-}{}{}vars@{TwoDfold\_\discretionary {-}{}{}vars}|hyperpage}{148}
\indexentry{TwoDpfold\_\discretionary {-}{}{}solution@{TwoDpfold\_\discretionary {-}{}{}solution}|hyperpage}{150}
\indexentry{TwoDpfold\_\discretionary {-}{}{}vars@{TwoDpfold\_\discretionary {-}{}{}vars}|hyperpage}{151}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dfold.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dfold.h}|hyperpage}{153}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dpfold.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dpfold.h}|hyperpage}{155}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/alifold.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/alifold.h}|hyperpage}{156}
\indexentry{alifold.h@{alifold.h}!update\_\discretionary {-}{}{}alifold\_\discretionary {-}{}{}params@{update\_\discretionary {-}{}{}alifold\_\discretionary {-}{}{}params}|hyperpage}{158}
\indexentry{update\_\discretionary {-}{}{}alifold\_\discretionary {-}{}{}params@{update\_\discretionary {-}{}{}alifold\_\discretionary {-}{}{}params}!alifold.h@{alifold.h}|hyperpage}{158}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/cofold.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/cofold.h}|hyperpage}{159}
\indexentry{cofold.h@{cofold.h}!get\_\discretionary {-}{}{}monomere\_\discretionary {-}{}{}mfes@{get\_\discretionary {-}{}{}monomere\_\discretionary {-}{}{}mfes}|hyperpage}{160}
\indexentry{get\_\discretionary {-}{}{}monomere\_\discretionary {-}{}{}mfes@{get\_\discretionary {-}{}{}monomere\_\discretionary {-}{}{}mfes}!cofold.h@{cofold.h}|hyperpage}{160}
\indexentry{cofold.h@{cofold.h}!initialize\_\discretionary {-}{}{}cofold@{initialize\_\discretionary {-}{}{}cofold}|hyperpage}{160}
\indexentry{initialize\_\discretionary {-}{}{}cofold@{initialize\_\discretionary {-}{}{}cofold}!cofold.h@{cofold.h}|hyperpage}{160}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/convert\_\discretionary {-}{}{}epars.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/convert\_\discretionary {-}{}{}epars.h}|hyperpage}{161}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/data\_\discretionary {-}{}{}structures.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/data\_\discretionary {-}{}{}structures.h}|hyperpage}{162}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/dist\_\discretionary {-}{}{}vars.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/dist\_\discretionary {-}{}{}vars.h}|hyperpage}{165}
\indexentry{dist\_\discretionary {-}{}{}vars.h@{dist\_\discretionary {-}{}{}vars.h}!edit\_\discretionary {-}{}{}backtrack@{edit\_\discretionary {-}{}{}backtrack}|hyperpage}{165}
\indexentry{edit\_\discretionary {-}{}{}backtrack@{edit\_\discretionary {-}{}{}backtrack}!dist_vars.h@{dist\_\discretionary {-}{}{}vars.h}|hyperpage}{165}
\indexentry{dist\_\discretionary {-}{}{}vars.h@{dist\_\discretionary {-}{}{}vars.h}!cost\_\discretionary {-}{}{}matrix@{cost\_\discretionary {-}{}{}matrix}|hyperpage}{165}
\indexentry{cost\_\discretionary {-}{}{}matrix@{cost\_\discretionary {-}{}{}matrix}!dist_vars.h@{dist\_\discretionary {-}{}{}vars.h}|hyperpage}{165}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/duplex.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/duplex.h}|hyperpage}{167}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/edit\_\discretionary {-}{}{}cost.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/edit\_\discretionary {-}{}{}cost.h}|hyperpage}{168}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/energy\_\discretionary {-}{}{}const.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/energy\_\discretionary {-}{}{}const.h}|hyperpage}{169}
\indexentry{energy\_\discretionary {-}{}{}const.h@{energy\_\discretionary {-}{}{}const.h}!GASCONST@{GASCONST}|hyperpage}{169}
\indexentry{GASCONST@{GASCONST}!energy_const.h@{energy\_\discretionary {-}{}{}const.h}|hyperpage}{169}
\indexentry{energy\_\discretionary {-}{}{}const.h@{energy\_\discretionary {-}{}{}const.h}!K0@{K0}|hyperpage}{169}
\indexentry{K0@{K0}!energy_const.h@{energy\_\discretionary {-}{}{}const.h}|hyperpage}{169}
\indexentry{energy\_\discretionary {-}{}{}const.h@{energy\_\discretionary {-}{}{}const.h}!INF@{INF}|hyperpage}{169}
\indexentry{INF@{INF}!energy_const.h@{energy\_\discretionary {-}{}{}const.h}|hyperpage}{169}
\indexentry{energy\_\discretionary {-}{}{}const.h@{energy\_\discretionary {-}{}{}const.h}!FORBIDDEN@{FORBIDDEN}|hyperpage}{169}
\indexentry{FORBIDDEN@{FORBIDDEN}!energy_const.h@{energy\_\discretionary {-}{}{}const.h}|hyperpage}{169}
\indexentry{energy\_\discretionary {-}{}{}const.h@{energy\_\discretionary {-}{}{}const.h}!BONUS@{BONUS}|hyperpage}{170}
\indexentry{BONUS@{BONUS}!energy_const.h@{energy\_\discretionary {-}{}{}const.h}|hyperpage}{170}
\indexentry{energy\_\discretionary {-}{}{}const.h@{energy\_\discretionary {-}{}{}const.h}!NBPAIRS@{NBPAIRS}|hyperpage}{170}
\indexentry{NBPAIRS@{NBPAIRS}!energy_const.h@{energy\_\discretionary {-}{}{}const.h}|hyperpage}{170}
\indexentry{energy\_\discretionary {-}{}{}const.h@{energy\_\discretionary {-}{}{}const.h}!TURN@{TURN}|hyperpage}{170}
\indexentry{TURN@{TURN}!energy_const.h@{energy\_\discretionary {-}{}{}const.h}|hyperpage}{170}
\indexentry{energy\_\discretionary {-}{}{}const.h@{energy\_\discretionary {-}{}{}const.h}!MAXLOOP@{MAXLOOP}|hyperpage}{170}
\indexentry{MAXLOOP@{MAXLOOP}!energy_const.h@{energy\_\discretionary {-}{}{}const.h}|hyperpage}{170}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/findpath.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/findpath.h}|hyperpage}{171}
\indexentry{findpath.h@{findpath.h}!find\_\discretionary {-}{}{}saddle@{find\_\discretionary {-}{}{}saddle}|hyperpage}{171}
\indexentry{find\_\discretionary {-}{}{}saddle@{find\_\discretionary {-}{}{}saddle}!findpath.h@{findpath.h}|hyperpage}{171}
\indexentry{findpath.h@{findpath.h}!get\_\discretionary {-}{}{}path@{get\_\discretionary {-}{}{}path}|hyperpage}{172}
\indexentry{get\_\discretionary {-}{}{}path@{get\_\discretionary {-}{}{}path}!findpath.h@{findpath.h}|hyperpage}{172}
\indexentry{findpath.h@{findpath.h}!free\_\discretionary {-}{}{}path@{free\_\discretionary {-}{}{}path}|hyperpage}{172}
\indexentry{free\_\discretionary {-}{}{}path@{free\_\discretionary {-}{}{}path}!findpath.h@{findpath.h}|hyperpage}{172}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold.h}|hyperpage}{173}
\indexentry{fold.h@{fold.h}!parenthesis\_\discretionary {-}{}{}structure@{parenthesis\_\discretionary {-}{}{}structure}|hyperpage}{175}
\indexentry{parenthesis\_\discretionary {-}{}{}structure@{parenthesis\_\discretionary {-}{}{}structure}!fold.h@{fold.h}|hyperpage}{175}
\indexentry{fold.h@{fold.h}!parenthesis\_\discretionary {-}{}{}zuker@{parenthesis\_\discretionary {-}{}{}zuker}|hyperpage}{175}
\indexentry{parenthesis\_\discretionary {-}{}{}zuker@{parenthesis\_\discretionary {-}{}{}zuker}!fold.h@{fold.h}|hyperpage}{175}
\indexentry{fold.h@{fold.h}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move}|hyperpage}{175}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move}!fold.h@{fold.h}|hyperpage}{175}
\indexentry{fold.h@{fold.h}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move\_\discretionary {-}{}{}pt@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move\_\discretionary {-}{}{}pt}|hyperpage}{176}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move\_\discretionary {-}{}{}pt@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move\_\discretionary {-}{}{}pt}!fold.h@{fold.h}|hyperpage}{176}
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\indexentry{loop\_\discretionary {-}{}{}energy@{loop\_\discretionary {-}{}{}energy}!fold.h@{fold.h}|hyperpage}{176}
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