Package: barriers Version: 1.8.1-1 Architecture: amd64 Maintainer: Ronny Lorenz Installed-Size: 175 Depends: libc6 (>= 2.14), perl Filename: ./amd64/barriers_1.8.1-1_amd64.deb Size: 59274 MD5sum: 9a749b02fe05b4afd10e41dc3a8402c7 SHA1: b59e0b779f9f2830d67dc1a9692702929e60e049 SHA256: 9bfb39a64c12604740075d7b356800f915ee70c1432265a0f262d174b2552865 Section: science Priority: optional Homepage: http://www.tbi.univie.ac.at/RNA/Barriers Description: Compute local minima and energy barriers of a landscape The program barriers reads an energy sorted list of conformations of a landscape, and computes local minima and energy barriers of the landscape. For RNA secondary structures, suitable input is produced by RNAsubopt For each local minimum found it prints to stdout, the conformation of the minimum, its energy, the number of the "parent"-minimum it merges with, and the height of the energy barrier. Additional information on each minimum, such as saddle point conformation and basin sizes can be included via options. A PostScript drawing of the resulting tree is written to "tree.ps" in the current directory. Package: barriers Version: 1.8.1-1 Architecture: i386 Maintainer: Ronny Lorenz Installed-Size: 169 Depends: libc6 (>= 2.7), perl Filename: ./i386/barriers_1.8.1-1_i386.deb Size: 56162 MD5sum: ca7029cb38960abccbc4e7e0de73f478 SHA1: aea0225a3a52ac844c7e977cba0068b7b9846b20 SHA256: a468a435f2be98bbd928fedc9c3ca6659021103f276ed86d58abf71b5ebef387 Section: science Priority: optional Homepage: http://www.tbi.univie.ac.at/RNA/Barriers Description: Compute local minima and energy barriers of a landscape The program barriers reads an energy sorted list of conformations of a landscape, and computes local minima and energy barriers of the landscape. For RNA secondary structures, suitable input is produced by RNAsubopt For each local minimum found it prints to stdout, the conformation of the minimum, its energy, the number of the "parent"-minimum it merges with, and the height of the energy barrier. Additional information on each minimum, such as saddle point conformation and basin sizes can be included via options. A PostScript drawing of the resulting tree is written to "tree.ps" in the current directory. Package: mlapack-dev Source: mlapack Version: 0.8.1-2 Architecture: amd64 Maintainer: Maho Nakata Installed-Size: 121077 Depends: libc6 (>= 2.14), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), libgomp1, libquadmath0, libgmp-dev, libmpfr-dev, libmpc-dev, libqd-dev Conflicts: mlapack-dev Provides: mlapack-dev Filename: ./amd64/mlapack-dev_0.8.1-2_amd64.deb Size: 27068618 MD5sum: 19000ea89a3de84c94672e8a678cb9b1 SHA1: 1b6178e708fb86e197a12759c8bb565dcd01a793 SHA256: a7f330d62b331bdb17a286e32715e84aeb862f4d23f933772b1d101d9fe4d854 Section: devel Priority: optional Description: mlapack - MPACK multi precision linear algebra package development files The MPACK is a multiprecision linear algebra package based on BLAS and LAPACK. This package is rewritten in C++, and supports several high precision libraries like GMP, MPFR and QD etc so that users can choose for user's convenience. The MPACK is a free software (2-clause BSD style license with original license by LAPACK). Package: mlapack-dev Source: mlapack Version: 0.8.1-2 Architecture: i386 Maintainer: Maho Nakata Installed-Size: 99901 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), libgomp1, libquadmath0, libgmp-dev, libmpfr-dev, libmpc-dev, libqd-dev Conflicts: mlapack-dev Provides: mlapack-dev Filename: ./i386/mlapack-dev_0.8.1-2_i386.deb Size: 24872276 MD5sum: a67f6a5e4218e02a17f44ea67dff653d SHA1: 8ea15cf48ccca2ef2c07492a41577cdb7debbeac SHA256: ef1151a29744226f730d8dcd6d58e660b509ea05b5277f9547ae724be0669d4b Section: devel Priority: optional Description: mlapack - MPACK multi precision linear algebra package development files The MPACK is a multiprecision linear algebra package based on BLAS and LAPACK. This package is rewritten in C++, and supports several high precision libraries like GMP, MPFR and QD etc so that users can choose for user's convenience. The MPACK is a free software (2-clause BSD style license with original license by LAPACK). Package: mpack-dev Source: mpack Version: 0.8.0 Architecture: amd64 Maintainer: Gregor Entzian Installed-Size: 239230 Depends: libc6 (>= 2.14), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), libquadmath0-dbg, libgmp-dev, libmpfr-dev, libmpc-dev, libqd-dev Conflicts: mpack-dev Provides: mpack-dev Filename: ./amd64/mpack-dev_0.8.0_amd64.deb Size: 52082428 MD5sum: f5d8ac673ebe2905babee0c963be59f8 SHA1: 84b14ccb5c1964bc3f6f09624c343402f37a814b SHA256: cd52bcbceae6891a9d451e0baa2d80af37b1281be226ac81cbe6ca391f887bc5 Section: devel Priority: optional Description: mpack - mpack development files The MPACK is a multipricision linear algebra package based on BLAS and LAPACK. This package is rewritten in C++, and supports several high precision libraries like GMP, MPFR and QD etc so that users can choose for user's convenience. The MPACK is a free software (2-clause BSD style license with original license by LAPACK). Package: mpack-dev Source: mpack Version: 0.8.0 Architecture: i386 Maintainer: Gregor Entzian Installed-Size: 197130 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), libquadmath0-dbg, libgmp-dev, libmpfr-dev, libmpc-dev, libqd-dev Conflicts: mpack-dev Provides: mpack-dev Filename: ./i386/mpack-dev_0.8.0_i386.deb Size: 46589700 MD5sum: 7e3eee94803387a1d08350f95b4e81ed SHA1: 471458a7db9e9bc1ffd7c7e14aeeba8a46814400 SHA256: 81e4c54ca85a4150b796fbaa351fb9805a9ec6fd215550eb7259d1e014c39647 Section: devel Priority: optional Description: mpack - mpack development files The MPACK is a multipricision linear algebra package based on BLAS and LAPACK. This package is rewritten in C++, and supports several high precision libraries like GMP, MPFR and QD etc so that users can choose for user's convenience. The MPACK is a free software (2-clause BSD style license with original license by LAPACK). Package: perl-rna Source: viennarna Version: 2.4.16-1 Architecture: amd64 Maintainer: Ronny Lorenz Installed-Size: 6351 Depends: perl (>= 5.18.2-2ubuntu1), perlapi-5.18.2, libc6 (>= 2.14), libgcc1 (>= 1:4.1.1), libgomp1 (>= 4.2.1), libgsl0ldbl (>= 1.9), libmpfr4 (>= 3.1.2), libstdc++6 (>= 4.1.1) Conflicts: vienna-rna (<< 2.2.1-2) Filename: ./amd64/perl-rna_2.4.16-1_amd64.deb Size: 1302404 MD5sum: 992d1f352aa16a1eb339163b95fc68d6 SHA1: d98aa0449b0d4d93aa4cdf4a00f3e10d41b8d68b SHA256: 500e082bec85c3c5bacea0b27efaabf3e0bce63577d18739479322b903dc9153 Section: perl Priority: optional Description: Perl bindings to ViennaRNA RNAlib The RNA module to access RNAlib C-library functions from within Perl scripts Package: perl-rna Source: viennarna Version: 2.4.16-1 Architecture: i386 Maintainer: Ronny Lorenz Installed-Size: 6345 Depends: perl (>= 5.18.2-2ubuntu1), perlapi-5.18.2, libc6 (>= 2.8), libgcc1 (>= 1:4.1.1), libgomp1 (>= 4.2.1), libgsl0ldbl (>= 1.9), libmpfr4 (>= 3.1.2), libstdc++6 (>= 4.1.1) Conflicts: vienna-rna (<< 2.2.1-2) Filename: ./i386/perl-rna_2.4.16-1_i386.deb Size: 1205168 MD5sum: 4c39c3eae0c13f5ab8f2f22044f592e2 SHA1: 24182510a5da94a54c811a969699820b717ec1b8 SHA256: 0fe914ac86e7228a62db78084580f872b7e5a97a32f18d8884c7bc279f62e030 Section: perl Priority: optional Description: Perl bindings to ViennaRNA RNAlib The RNA module to access RNAlib C-library functions from within Perl scripts Package: perl-rna-barrier Source: barriers Version: 1.8.1-1 Architecture: amd64 Maintainer: Ronny Lorenz Installed-Size: 52 Depends: perl, perl-rna Filename: ./amd64/perl-rna-barrier_1.8.1-1_amd64.deb Size: 6612 MD5sum: 41b6571d94d88205a64de35e6ad8c703 SHA1: eb2fbb20ba54e984eef259997304e0734bf970f3 SHA256: 0e5bb1b6f191009668dfa363f4d176593a88d86d06c99ed46847098761bdaf75 Section: perl Priority: optional Homepage: http://www.tbi.univie.ac.at/RNA/Barriers Description: Perl module and scripts for Barriers The RNA/barrier module and perl scripts to access some functionality of the Barriers program Package: perl-rna-barrier Source: barriers Version: 1.8.1-1 Architecture: i386 Maintainer: Ronny Lorenz Installed-Size: 52 Depends: perl, perl-rna Filename: ./i386/perl-rna-barrier_1.8.1-1_i386.deb Size: 6604 MD5sum: c463603f0fcf67d11bfb93e872230c5d SHA1: b791f938809dbab886bde64263c5415b6ce0e985 SHA256: cdbd984725eeeed5829f7574b3bb81061d91637362179e04125fa22de6d81491 Section: perl Priority: optional Homepage: http://www.tbi.univie.ac.at/RNA/Barriers Description: Perl module and scripts for Barriers The RNA/barrier module and perl scripts to access some functionality of the Barriers program Package: python-rna Source: viennarna Version: 2.4.16-1 Architecture: amd64 Maintainer: Ronny Lorenz Installed-Size: 6375 Depends: python (>= 2.7~), python (<< 2.8), python:any (>= 2.7.5-5~), libc6 (>= 2.14), libgcc1 (>= 1:4.1.1), libgomp1 (>= 4.2.1), libgsl0ldbl (>= 1.9), libmpfr4 (>= 3.1.2), libstdc++6 (>= 4.2.1) Conflicts: vienna-rna (<< 2.2.1-2) Filename: ./amd64/python-rna_2.4.16-1_amd64.deb Size: 1254528 MD5sum: 5d697e95a13baf8978c6562487cc7578 SHA1: b13ef431a1ef924ece301e347627e40bccc234ab SHA256: 0b979955332746bf1ad985e39492a7489dc37a82a4722de436c880aa460c74ca Section: python Priority: optional Description: Python 2 bindings to ViennaRNA RNAlib The RNA class to access RNAlib C-library functions from within Python 2 scripts Package: python-rna Source: viennarna Version: 2.4.16-1 Architecture: i386 Maintainer: Ronny Lorenz Installed-Size: 6285 Depends: python (<< 2.8), python (>= 2.7~), python:any (>= 2.7.5-5~), libc6 (>= 2.8), libgcc1 (>= 1:4.1.1), libgomp1 (>= 4.2.1), libgsl0ldbl (>= 1.9), libmpfr4 (>= 3.1.2), libstdc++6 (>= 4.2.1) Conflicts: vienna-rna (<< 2.2.1-2) Filename: ./i386/python-rna_2.4.16-1_i386.deb Size: 1167206 MD5sum: e83c459c372280f2134c6cfa3d9e674c SHA1: a28f4499da953b1c0a98022d9c5e98e2c3a1f12a SHA256: 990602df270e41a84c0ff28fd02a75106c93d6b66de89cf8020852712112e9f0 Section: python Priority: optional Description: Python 2 bindings to ViennaRNA RNAlib The RNA class to access RNAlib C-library functions from within Python 2 scripts Package: python3-rna Source: viennarna Version: 2.4.16-1 Architecture: amd64 Maintainer: Ronny Lorenz Installed-Size: 6417 Depends: python3 (>= 3.4~), python3 (<< 3.5), libc6 (>= 2.14), libgcc1 (>= 1:4.1.1), libgomp1 (>= 4.2.1), libgsl0ldbl (>= 1.9), libmpfr4 (>= 3.1.2), libstdc++6 (>= 4.2.1) Conflicts: vienna-rna (<< 2.2.1-2) Filename: ./amd64/python3-rna_2.4.16-1_amd64.deb Size: 1258266 MD5sum: 65488a8413d4c92d2bf488a432cb6e81 SHA1: 1e712e381b3ee551b08fc6e7e5566f6e7b8cc6f0 SHA256: 196c749be41ff00cb8970c647e6a8820f24917434eea73f7ff5722a39f2205e7 Section: python Priority: optional Description: Python 3 bindings to ViennaRNA RNAlib The RNA class to access RNAlib C-library functions from within Python 3 scripts Package: python3-rna Source: viennarna Version: 2.4.16-1 Architecture: i386 Maintainer: Ronny Lorenz Installed-Size: 6322 Depends: python3 (>= 3.4~), python3 (<< 3.5), libc6 (>= 2.8), libgcc1 (>= 1:4.1.1), libgomp1 (>= 4.2.1), libgsl0ldbl (>= 1.9), libmpfr4 (>= 3.1.2), libstdc++6 (>= 4.2.1) Conflicts: vienna-rna (<< 2.2.1-2) Filename: ./i386/python3-rna_2.4.16-1_i386.deb Size: 1170178 MD5sum: 8f291e0a84e07f73ca12f7777d238c2f SHA1: 25caa9ba8c9a37840857e386f6f2ad5c4c8c2c64 SHA256: 62fd3fa592f7286551095c117aa0f5c25c3f909dbf84957c578437d53dc9e992 Section: python Priority: optional Description: Python 3 bindings to ViennaRNA RNAlib The RNA class to access RNAlib C-library functions from within Python 3 scripts Package: treekin Version: 0.5.0-1 Architecture: amd64 Maintainer: Ronny Lorenz Installed-Size: 137 Depends: libc6 (>= 2.14), libgcc1 (>= 1:4.1.1), liblapack3, libstdc++6 (>= 4.1.1), libblas3, liblapacke, gfortran, mlapack-dev Filename: ./amd64/treekin_0.5.0-1_amd64.deb Size: 46148 MD5sum: 02c71bb63aa903815b4ea9f448d32fd6 SHA1: 74f41a2584c1023dfa8d6bd2ba4bbf172dd0530a SHA256: 83fc42726b83b7e6153be78affed14695e3050e44b311e57e0f64c399b448ec2 Section: science Priority: optional Homepage: http://www.tbi.univie.ac.at/RNA/Treekin Description: Efficient computation of RNA folding dynamics The program treekin computes folding dynamics on coarse grained version of an energy landscape, where all conformations belonging to the same local minimum have been contracted into a single macro-state. Treekin reads in the a list of local minima (macro-states) and effective refolding rates between these minima as computed by barriers --rates. Since the the number of macro-states is small (typically on the order of 100—1000), folding dynamics can be computed by direct numerical integration of the master equation conformations (i.e. diagonalization of the rate matrix). For detailed instructions see the man page. Package: treekin Version: 0.5.0-1 Architecture: i386 Maintainer: Ronny Lorenz Installed-Size: 131 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), liblapack3, libstdc++6 (>= 4.1.1), libblas3, liblapacke, gfortran, mlapack-dev Filename: ./i386/treekin_0.5.0-1_i386.deb Size: 43106 MD5sum: 71d501ba77d0d9765dcb7ea986326b03 SHA1: a4c4536ce83cc9c5b5cf1be0241865fe65d54fa6 SHA256: ec926dc296ec60517a52d4f6e501a00917eb0c3dd38904265f3aef942b8cedee Section: science Priority: optional Homepage: http://www.tbi.univie.ac.at/RNA/Treekin Description: Efficient computation of RNA folding dynamics The program treekin computes folding dynamics on coarse grained version of an energy landscape, where all conformations belonging to the same local minimum have been contracted into a single macro-state. Treekin reads in the a list of local minima (macro-states) and effective refolding rates between these minima as computed by barriers --rates. Since the the number of macro-states is small (typically on the order of 100—1000), folding dynamics can be computed by direct numerical integration of the master equation conformations (i.e. diagonalization of the rate matrix). For detailed instructions see the man page. Package: viennarna Version: 2.4.16-1 Architecture: amd64 Maintainer: Ronny Lorenz Installed-Size: 39841 Depends: libgomp1 (>= 4.4.5-1), libgsl0ldbl (>= 1.9), libmpfr4 (>= 3.1.2), libc6 (>= 2.14), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.8) Recommends: python-rna, perl-rna Breaks: vienna-rna (<< 2.2.1-2) Replaces: vienna-rna (<< 2.2.1-2) Filename: ./amd64/viennarna_2.4.16-1_amd64.deb Size: 2831968 MD5sum: 37474ec7b3e74613868f5805fea2aa53 SHA1: 59eb05fd4a8e8f06c838f5a1edef715c8ca5c48c SHA256: 44d9e4cb76e10412c6b131d9999d44c23891f7888950e75c469ebe8ee48ae57e Section: science Priority: optional Description: Vienna RNA Package - Core The Vienna RNA Package Core consists of several executable programs and various scripts for the prediction and comparison of RNA secondary structures. Package: viennarna Version: 2.4.16-1 Architecture: i386 Maintainer: Ronny Lorenz Installed-Size: 39189 Depends: libgomp1 (>= 4.4.5-1), libgsl0ldbl (>= 1.9), libmpfr4 (>= 3.1.2), libc6 (>= 2.8), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.8) Recommends: python-rna, perl-rna Breaks: vienna-rna (<< 2.2.1-2) Replaces: vienna-rna (<< 2.2.1-2) Filename: ./i386/viennarna_2.4.16-1_i386.deb Size: 2695322 MD5sum: 7144fdaf78244361b691732568f372e1 SHA1: e7c9f907f29dee9977e5e68e3be1466bb474d862 SHA256: fa1b37c597eab3009fa1ae9478b16213a17200fa73a9d79083e851e828627d35 Section: science Priority: optional Description: Vienna RNA Package - Core The Vienna RNA Package Core consists of several executable programs and various scripts for the prediction and comparison of RNA secondary structures. Package: viennarna-dev Source: viennarna Version: 2.4.16-1 Architecture: amd64 Maintainer: Ronny Lorenz Installed-Size: 27545 Depends: libgsl0-dev | libgsl-dev, libmpfr-dev Conflicts: vienna-rna (<< 2.2.1-2) Filename: ./amd64/viennarna-dev_2.4.16-1_amd64.deb Size: 12104610 MD5sum: c7010245de5c0cc701279db54a909c40 SHA1: eecd674e10a5cdf42871fb35173cca9386c878c7 SHA256: 40dcc202b70e012f664bd85a9dc8948bbd4a45ebdb32704ecacf29abe24e0d41 Section: devel Priority: optional Description: ViennaRNA Package - RNAlib Development files Header files and static RNAlib C-library of the ViennaRNA Package Package: viennarna-dev Source: viennarna Version: 2.4.16-1 Architecture: i386 Maintainer: Ronny Lorenz Installed-Size: 22960 Depends: libgsl0-dev | libgsl-dev, libmpfr-dev Conflicts: vienna-rna (<< 2.2.1-2) Filename: ./i386/viennarna-dev_2.4.16-1_i386.deb Size: 11962020 MD5sum: 3db0c4451de3e81b0eb1d54e771cab67 SHA1: 9e51cb82329fc637830fa4daf56338a56c68f17d SHA256: 761120934b944f547f2b5948d4bd8551a0ab9338480f679b2786836796b35136 Section: devel Priority: optional Description: ViennaRNA Package - RNAlib Development files Header files and static RNAlib C-library of the ViennaRNA Package Package: viennarna-doc Source: viennarna Version: 2.4.16-1 Architecture: all Maintainer: Ronny Lorenz Installed-Size: 30642 Conflicts: vienna-rna (<< 2.2.1-2) Filename: ./all/viennarna-doc_2.4.16-1_all.deb Size: 6764410 MD5sum: f6be1bac223c9d5f8b137c3b0b74200c SHA1: 00bd4fff590b83dcfa6284af7551d9b5a83fbe22 SHA256: b013ff2c7a455294f68f409a19bd638134caddd641653ccf9bd03747a9f583ad Section: doc Priority: optional Description: ViennaRNA Package - RNAlib Reference Manual Reference Manual for RNAlib C-library in PDF and HTML format