v1.3.1

Release corresponding to making repo public. Change since v1.3.0: Update to license.

SHAPE-directed folding and stochastic sampling

EternaFold release corresponding to Wayment-Steele, ... Das (2022) RNA secondary structure packages evaluated and improved by high-throughput experiments.

Major updates:

-Implements SHAPE-directed folding using learned SHAPE potentials.

-Implements stochastic structure sampling from distribution.

Minor updates:

• Includes FASTA-format files for all data used for training/testing EternaFold.

EternaFold, with LinearFold/LinearPartition patches

Provides patches for LinearFold and LinearPartition
README documents discrepancies between this and CONTRAfold codebase

EternaFold_1.1.0

Features

• Added LinearFold parameters

EternaFold_1.0.0

EternaFold multitask-learning RNA structure inference engine. Codebase corresponding to preprint, "RNA secondary structure algorithms ranked and improved by high-throughput experiments", Wayment-Steele, Kladwang, Eterna participants, Das, 2020.