Package: barriers Version: 1.8.1-1 Architecture: amd64 Maintainer: Ronny Lorenz Installed-Size: 176 Depends: libc6 (>= 2.14), perl Filename: ./amd64/barriers_1.8.1-1_amd64.deb Size: 61324 MD5sum: 9adbc221e88e05aa2ae8a385ccfab3b2 SHA1: 043940d3a34872e7ea52806351f61c673e1ffdf4 SHA256: 301a125a74ac55af2dbce30f5fbbd4d880a21fb8e7c9a7a53b68a2aec66b3f16 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: 178 Depends: libc6 (>= 2.7), perl Filename: ./i386/barriers_1.8.1-1_i386.deb Size: 61620 MD5sum: eafbcb6f118f9a1186fc8a23cd8391ef SHA1: 9fa646b8f3732db45ff54b3b74a4a5c477a3456a SHA256: f875a93960781d0f79f6b8408c3a6f589d80b59e06ea46f3363e3c94bf9440b8 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: 122476 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: 27971470 MD5sum: 32bfd9394c1d5e8e84da8147f4f9f0fe SHA1: 258d8757242b6372cd5ba092930094337e2b3a43 SHA256: b24c50912e8415676f2e5eda1e842faa30b61e4b96919daacaffe7b50d3f6c4d 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: 103770 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: 24843724 MD5sum: fd7159ce58250b74e317256b65912ba7 SHA1: edc08c5984669c22f42857e60016790d8fad0ad1 SHA256: 908f9cedf015480ab79e6fe32255318ba37ea95fd013106dff2629744ce6811b 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: 242001 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: 53479068 MD5sum: 1a4da3481780c9aa56d89de2eea9c228 SHA1: 01b34f0fd1fe0d6abdd1c882f68c774c5f6db460 SHA256: 04143b4cc76ba0634e842c9c3317104bc486d3c2b7ec5d04508503367c4dd321 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: 204850 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: 45713022 MD5sum: 7d92d25ba1a0823ba06d308b6c391790 SHA1: c37dd8424331e6826d25813bc1b1400131d53ca2 SHA256: 43b226fcd540c6e52590e7b0d9fe130c070f9df47da4eb72ff600ffa86ace7ad 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: 6519 Depends: perl (>= 5.20.2-3), perlapi-5.20.2, libc6 (>= 2.14), libgcc1 (>= 1:4.1.1), libgmp10, libgomp1 (>= 4.9), 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: 1335648 MD5sum: 157343795bacddcfcc2345555c6cacf7 SHA1: b9f86f17bf4c0898b5434752adc7b7936944384a SHA256: 603da41a3db9f00999a9ef6d09881009c43b3f8e27974495c4b09f3276af2b95 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: 6624 Depends: perl (>= 5.20.2-3), perlapi-5.20.2, libc6 (>= 2.8), libgcc1 (>= 1:4.1.1), libgmp10, libgomp1 (>= 4.9), 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: 1285542 MD5sum: 9dee564140459cb3be76a7396ffb94a8 SHA1: e1276f62a91a4d72cf617bc9a7c02cfab7a9ab39 SHA256: 0a3a4060cdb158f5e95c6f8b8e4bc32600bc09fbd212642266043bb2d8366e10 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: 7566 MD5sum: c8fc8c911135e9fb5bdabdf24036231c SHA1: 8c928b82b890843dc38df2badca131780bcbefc4 SHA256: 571de5e16d207c3f622ffbc40e74628920d89df69f46ea2ed75ea6acc9454e79 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: 7586 MD5sum: 79669c2c544ecd2c9bd1047fdae22e1b SHA1: aec109c823cdc29435addf74cfddcd7b00afb5a1 SHA256: 8fdb25ca68ef16b640b9b1c6a387719b9e38be30a676a049295850de1944f8a7 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: 6528 Depends: python (<< 2.8), python (>= 2.7~), python:any (>= 2.7.5-5~), libc6 (>= 2.14), libgcc1 (>= 1:4.1.1), libgmp10, libgomp1 (>= 4.9), 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: 1296224 MD5sum: da6f4ed7a786181e92f526ab23acddd1 SHA1: 1b7d454e749443a580d9276b62d7492f3a49e285 SHA256: b29fc69b1264eb669dcc4b40ec64b97ee4b4f14807c9d1ad56f8e9801505f680 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: 6495 Depends: python (<< 2.8), python (>= 2.7~), python:any (>= 2.7.5-5~), libc6 (>= 2.8), libgcc1 (>= 1:4.1.1), libgmp10, libgomp1 (>= 4.9), 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: 1242902 MD5sum: cfce65ce5b54c5f7c7527ddde687747f SHA1: 1e7ef001df4c6d9cbc1980e280ecbcc74d5bffe6 SHA256: 7a22d3a740de35bcd0d38e1e78dd563b1baa1f93271f73a0aaa28e0dcdd6de71 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: 6562 Depends: python3 (<< 3.5), python3 (>= 3.4~), libc6 (>= 2.14), libgcc1 (>= 1:4.1.1), libgmp10, libgomp1 (>= 4.9), 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: 1301106 MD5sum: 16e6f6a52e00b3d6fc3f07b1e0272e3c SHA1: dea2201af3f0db2b550f4869328e248e8655ff6a SHA256: fc03bfc56ca1783689d98cd826b58d8fabe2adb953c1fa24a7db5e6e3a836465 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: 6532 Depends: python3 (<< 3.5), python3 (>= 3.4~), libc6 (>= 2.8), libgcc1 (>= 1:4.1.1), libgmp10, libgomp1 (>= 4.9), 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: 1249584 MD5sum: 6fccb3d5fedf4072adde0d738cc912eb SHA1: a497df5c8114a752db6919043bbadf0cea6efdb9 SHA256: 12ee5f5ec9630914f41b1ecb38aa081ba7f8f9813cb4b3b0ecc5c0984483c381 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: 138 Depends: libblas3, libc6 (>= 2.14), libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.3), liblapack3, libquadmath0 (>= 4.6), libstdc++6 (>= 4.9), liblapacke, gfortran, mlapack-dev Filename: ./amd64/treekin_0.5.0-1_amd64.deb Size: 47382 MD5sum: fa72f7f3b256080dfc3e420f21b47ae9 SHA1: 2df9a8eae09204c55b0005cc0fc9716214552a27 SHA256: 81a87f45b26a893cbcdb08dff905afab73b423288f21afe077ec4c39979172ae 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: 140 Depends: libblas3, libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.3), liblapack3, libquadmath0 (>= 4.6), libstdc++6 (>= 4.9), liblapacke, gfortran, mlapack-dev Filename: ./i386/treekin_0.5.0-1_i386.deb Size: 47200 MD5sum: f08dbf96eb7175284229f5ff5cd4ffc1 SHA1: 61f655edd312a7d52fc24c8f00af061481ce3c75 SHA256: 049112df6cfe781fdd4e4e3374206c3efa6e7d5607290706ba5f26a1664b80f4 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: 39735 Depends: libgomp1 (>= 4.9), libgsl0ldbl (>= 1.9), libmpfr4 (>= 3.1.2), libc6 (>= 2.14), libgcc1 (>= 1:4.1.1), libgmp10, 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: 2893204 MD5sum: c8bec34e9889becea10d01d852845ca1 SHA1: 4bae7d43e42acf90bcddf8033a1eef77e4bff83a SHA256: 4184992d22ed3bc4265de8a8d3170ea396ab6f1c2d1321bfa4f8eee7026bf83a 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: 39436 Depends: libgomp1 (>= 4.9), libgsl0ldbl (>= 1.9), libmpfr4 (>= 3.1.2), libc6 (>= 2.8), libgcc1 (>= 1:4.1.1), libgmp10, 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: 2792412 MD5sum: 2db2b8e778898a06189bb30e5999593d SHA1: 068c01b5da114ea503e4118929bda53b60507869 SHA256: c30f3350d706e563d8331bd15270deed556ced1e4773118fa2f3ed1dc5644d7d 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: 31612 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: 17109186 MD5sum: 675c87127f29a115a81234caaef4dab6 SHA1: 013a0ac8f5a96a96d05f0fdd64536cf9784e06ef SHA256: f690b2878be5b8ecc7f76ad40961012512a18d9d2f65772d47d1225645be2cba 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: 26236 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: 16613902 MD5sum: addbf555ddb34880a12456fb1933415f SHA1: 2cb8ff880f712a7a7af2602d33da162f781c4947 SHA256: 54e0c86169496b6590993e39a718fcb0d1e9fc16951bb9fe083f38c554a02fc4 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: 30715 Conflicts: vienna-rna (<< 2.2.1-2) Filename: ./all/viennarna-doc_2.4.16-1_all.deb Size: 6786100 MD5sum: 4bbc89a2f5c45a2a0d88061341d57ed8 SHA1: fa8f4e25a745707b2f997f799adba5f73590770c SHA256: e0c70fce252f45d539d8f98edc0532a2c9e4a00f090e1da6d84860c7c3b6a7f5 Section: doc Priority: optional Description: ViennaRNA Package - RNAlib Reference Manual Reference Manual for RNAlib C-library in PDF and HTML format