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https://github.com/ViennaRNA/ViennaRNA
25 March 2024, 05:18:21 UTC
Release v2.1.0 created by Ronny Lorenz on 25 January 2013, 13:50:52 UTC 
Version 2.1.0:

Package:
	- The auxilary energy parameter files in the source tree now reside in the 'misc' directory.
	  They are, however, still installed at the same locations as in previous versions of the Package.
	- To enable fast plotting of RNA2Dfold output we now also provide two gri-scripts
	  "2Dlandscape_mfe.gri" and "2Dlandscape_pf.gri". To use them, simply redirect the output
	  of RNA2Dfold into a text file and then call the appropriate script with the RNA2Dfold output
	  filename as first parameter, e.g.:

	  $ ./2Dlandscape_mfe.gri my_2Dfold_output.txt

	  This will create a postscript file named "my_2Dfold_output.txt.ps" that displays the MFE
	  output in a nice landscape like manner
	- the Utils script "relplot.pl" got a new commandline option "-a" that enables annotation
          of the accessibility in the structure plot
        - some changes in the build process now enable easier cross compilation of the Package
        - The example sourcecode in the reference manual got an update to comply with the specifications
          of ViennaRNA Package 2.x

Programs:
        - G-Quadruplex prediction support in RNAfold, RNAcofold, RNALfold, RNAalifold, RNAeval and RNAplot
          this introduces a new commandline option '--gquad/-g' that enables G-quadruplex prediction. The
          dot-bracket notation for the structure output now contains an additional character '+' that
          indicates the presence of such a G-tetrad. Consecutive '+' signs always come in sets of 4
          interspaced by some '.', marking the four G-runs and its linker sequences that comprise the
          quadruplex, respectively.
        - changes in RNAPKplex behavior and commandline options
        - new features and bugfixes in RNAplex and RNAsnoop
        - warning messages for all programs if an unsupported dangle option is selected

Library:
        - LPfold got a new option to output its computations in split-mode
        - several G-Quadruplex related functions were introduced with this release
        - several functions for moves in an RNA landscape were introduced
        - a new function in alipfold.c now enables access to the partition function matrices of
          alipf_fold()
        - a different numeric approach was implement for concentration dependend co-folding to
          avoid instabilities which occured under certain circumstances
Target: 06198b62610218cd1f967ea602236920e978a4b0
Directory: 18c9b23aa974c3b01dbf0e118140aaee0e469c23
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