ViennaRNA v0.11.1

Diff since v0.11.0

Merged pull requests:

• Version 0.11.1, update ViennaRNA_jll to v2.6.4 (#22) (@marcom)

ViennaRNA v0.11.0

Diff since v0.10.1

Closed issues:

• Segfault for plot_coords("()") (#13)

Merged pull requests:

• Update to ViennaRNA 2.6 (#15) (@marcom)

ViennaRNA v0.10.1

Diff since v0.10.0

Merged pull requests:

• plot_coords: avoid segfault for zero-length hairpins for some plot types (#16) (@marcom)
• v0.10.1 (#17) (@marcom)

ViennaRNA v0.10.0

Diff since v0.9.0

Important changes

There is a new way of changing energy parameters that more closely mirrors the ViennaRNA API and allows for higher performance. Now energy parameters are changed by calling e.g. ViennaRNA.params_load(:RNA_Turner1999) or ViennaRNA.params_load_RNA_Turner1999(). All FoldCompounds constructed afterwards will then use these parameters. The old way of setting the parameters via a keyword argument in the constructor FoldCompound(...; params=:RNA_Turner1999) does not work anymore.

Closed issues:

• how can I improve it's performence? (#12)

ViennaRNA v0.9.0

Diff since v0.8.1

• new functions

  • mfe_window
  • mfe_window_channel
  • ViennaRNA.init_rand_seed

• set options with Symbols instead of Integers in various functions

• FoldCompound

  • allow setting max_bp_span and window_size

• sample_structures is the new name for pbacktrack (the same as in RNAstructure.jl and LinearFold.jl)

• plot_coords defaults to the :puzzler plot type (like in the ViennaRNA C library)

Closed issues:

• DNA parameters (#10)

Merged pull requests:

• circular=false in Readme (#11) (@cossio)

ViennaRNA v0.8.1

Diff since v0.8.0

Closed issues:

• plot_structure_makie is very slow on the first run (#5)
• Graphic dependencies are quite heavy (#8)

ViennaRNA v0.8.0

Diff since v0.7.0

• move secondary structure plotting functionality to PlotRNA.jl package
• this greatly reduces package loading times (10s to 0.5s on my machine)

ViennaRNA v0.7.0

Diff since v0.6.6

• support for ViennaRNA-2.5.1

ViennaRNA v0.6.6

Diff since v0.6.5

ViennaRNA v0.6.5

Diff since v0.6.4

ViennaRNA v0.6.4

Diff since v0.6.3

Closed issues:

• Feature request: Alifold (#7)

ViennaRNA v0.6.3

• support for alifold mode (comparative folding with a MSA)

Diff since v0.6.2

ViennaRNA v0.6.2

Diff since v0.6.1

ViennaRNA v0.6.1

Changes since v0.5.0:

• experimental plot_structure and plot_structure_makie functions to draw secondary structures with Cairo
• support for circular strands
• initial support for multiple strands (no concentration calculation yet)
• added heat_capacity function
• plot_coords defaults to the 'simple' layout algorithm

Diff since v0.6.0

ViennaRNA v0.6.0

Diff since v0.5.0

Closed issues:

• Basepair probability vector and plotting RNA structures (#3)

Merged pull requests:

• Add plot_structure function using Makie.jl (#4) (@timoleistner)

ViennaRNA v0.5.0

• bpp now returns a symmetric matrix of basepair probabilities
• new prob_of_basepairs function that calculates the probability of every basepair or unpaired base for a (sequence, structure) pair
• new plot_structure function that implements a simple form of secondary structure plotting with base coloring (see issue #3)

Diff since v0.4.1

ViennaRNA v0.4.1

Diff since v0.4.0

ViennaRNA v0.4.0

• energy parameter set and temperature used in the calculations can be set for a FoldCompound
• uniq_ML argument to FoldCompound is now of type Bool

Diff since v0.3.1

ViennaRNA v0.3.1

Diff since v0.3.0

• fix memory leaks in pbacktrack, subopt, subopt_zuker

Closed issues:

• Fails to precompile on CI (#1)

ViennaRNA.jl 0.3.0

• use ViennaRNA_jll v2.5.0
• pre-generate bindings with Clang.jl instead of CBinding (CBinding required C standard header files installed at runtime)
• new functions: plot_coords, neighbors

Fixes #1