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Table 2 Multiple Sequence Methods.

From: RNAstructure: software for RNA secondary structure prediction and analysis

Feature:

Text Interface Program:

JAVA/Windows GUI Menu Item:

Class Library and Function Name:

Dynalign [23, 41, 46]

dynalign

Dynalign RNA

Dynalign_object::Dynalign

OligoWalk [31–33]

OligoWalk

OligoWalk

Oligowalk_object::Oligowalk

OligoScreen [55]

oligoscreen

OligoScreen

Oligowalk_object::OligoScreen

Bimolecular structure prediction with intramolecular pairs [33]

bifold

Fold RNA

Bimolecular

HybridRNA::FoldBimolecular

PARTS [24, 48]

PARTS

-

-

Bimolecular partition function (no intramolecular pairs) [31]

bipartition

Partition

Function RNA

Bimolecular

HybridRNA::PartitionFunctionBimolecular

Bimolecular structure prediction without intramolecular pairs

DuplexFold

-

HybridRNA::FoldDuplex