BSD Portsbiology/viennarna 2.7.2 FreeBSD
Alignment tools for the structural analysis of RNA
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- License
- ViennaRNALicense
- Categories
- biology
- Package size
- 16901.4 KiB, 137709.9 KiB installed
Description
The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
RNA secondary structure prediction through energy minimization is the most used function in the package. We provide three kinds of dynamic programming algorithms for structure prediction: the minimum free energy algorithm of (Zuker & Stiegler 1981) which yields a single optimal structure, the partition function algorithm of (McCaskill 1990) which calculates base pair probabilities in the thermodynamic ensemble, and the suboptimal folding algorithm of (Wuchty et.al 1999) which generates all suboptimal structures within a given energy range of the optimal energy. For secondary structure comparison, the package contains several measures of distance (dissimilarities) using either string alignment or tree-editing (Shapiro & Zhang 1990). Finally, we provide an algorithm to design sequences with a predefined structure (inverse folding).
In the other systems
The newest version among them is 2.7.2, as upstream numbers it.
| System | Port | Version | Vulnerabilities | Status | Maintainer | Last update |
|---|---|---|---|---|---|---|
| FreeBSD | biology/viennarna | 2.7.2 newest | none known | - | [email protected] | - |
| DragonFly | biology/viennarna | 2.7.0_1 | none known | - | [email protected] | - |
| HardenedBSD | biology/viennarna | 2.7.2 newest | no data | - | [email protected] | - |
| GhostBSD | biology/viennarna | 2.7.2 newest | no data | - | [email protected] | - |
Install
Binary package:
pkg install viennarnaFrom the ports tree:
cd /usr/ports/biology/viennarna/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= viennarna>0:biology/viennarnaPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 2.7.2 | 2.7.2 | 2.5.1 | 2.7.0_1 | 2.7.2 |
| FreeBSD:14:quarterly | 2.7.2 | 2.7.2 | n/a | 2.7.0_1 | 2.7.2 |
| FreeBSD:15:latest | 2.7.2 | 2.7.2 | n/a | - | - |
| FreeBSD:15:quarterly | 2.7.2 | 2.7.2 | n/a | n/a | n/a |
| FreeBSD:16:latest | 2.7.2 | 2.7.2 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependency graph
Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.
Dependencies
As this port's Makefile names them.
Build 5
bash: shells/bashlapacke>0: math/lapackelibgd>0: graphics/gdswig: devel/swigxxd: sysutils/xxd
Library 5
libdlib.so: science/dlib-cpplibgmp.so: math/gmplibgsl.so: math/gslliblapack.so: math/lapacklibmpfr.so: math/mpfr
The full lists below include those, and their dependencies in turn.
Build dependencies 53
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/zstd
- databases/sqlite3
- devel/autoconf
- devel/autoconf-switch
- devel/automake
- devel/binutils
- devel/bison
- devel/gettext-runtime
- devel/gmake
- devel/libedit
- devel/libtextstyle
- devel/libtool
- devel/m4
- devel/pcre2
- devel/pkgconf
- devel/swig
- graphics/gd
- graphics/giflib
- graphics/jbigkit
- graphics/jpeg-turbo
- graphics/lerc
- graphics/png
- graphics/tiff
- graphics/webp
- lang/gcc14
- lang/perl5.42
- lang/tcl86
- math/blas
- math/gmp
- math/gsl
- math/lapack
- math/lapacke
- math/libtommath
- math/mpc
- math/mpfr
- print/freetype2
- print/indexinfo
- science/dlib-cpp
- shells/bash
- sysutils/xxd
- textproc/expat2
- x11-fonts/fontconfig
- x11/libICE
- x11/libSM
- x11/libX11
- x11/libXau
- x11/libXdmcp
- x11/libXext
- x11/libxcb
- x11/xorgproto
Run dependencies 28
- archivers/liblz4
- archivers/zstd
- databases/sqlite3
- devel/binutils
- devel/libedit
- graphics/giflib
- graphics/jpeg-turbo
- graphics/png
- lang/gcc14
- lang/perl5.42
- lang/tcl86
- math/blas
- math/gmp
- math/gsl
- math/lapack
- math/libtommath
- math/mpc
- math/mpfr
- print/indexinfo
- science/dlib-cpp
- x11/libICE
- x11/libSM
- x11/libX11
- x11/libXau
- x11/libXdmcp
- x11/libXext
- x11/libxcb
- x11/xorgproto
Required by 1
Configuration
Options name: biology_viennarna
| Option | Default | Description |
|---|---|---|
| DOCS | off | Build and/or install documentation |
| EXAMPLES | off | Build and/or install examples |
- USES
- autoreconf bison compiler:c++17-lang fortran gmake libtool localbase perl5 pkgconfig xorg
- Service scripts
- none
- Conflicts with
- g2
Files
Manual pages 33
- AnalyseDists(1)
- AnalyseSeqs(1)
- Kinfold(1)
- RNA2Dfold(1)
- RNALalifold(1)
- RNALfold(1)
- RNAPKplex(1)
- RNAaliduplex(1)
- RNAalifold(1)
- RNAcofold(1)
- RNAdistance(1)
- RNAdos(1)
- RNAduplex(1)
- RNAeval(1)
- RNAfold(1)
- RNAforester(1)
- RNAheat(1)
- RNAinverse(1)
- RNAlocmin(1)
- RNAmultifold(1)
- RNApaln(1)
- RNAparconv(1)
- RNApdist(1)
- RNAplex(1)
- RNAplfold(1)
- RNAplot(1)
- RNApvmin(1)
- RNAsnoop(1)
- RNAsubopt(1)
- RNAup(1)
- RNAxplorer(1)
- ct2db(1)
- kinwalker(1)
pkg-plist 325
- bin/AnalyseDists
- bin/AnalyseSeqs
- bin/Kinfold
- bin/RNA2Dfold
- bin/RNALalifold
- bin/RNALfold
- bin/RNAPKplex
- bin/RNAaliduplex
- bin/RNAalifold
- bin/RNAcofold
- bin/RNAconsensus
- bin/RNAdistance
- bin/RNAdos
- bin/RNAduplex
- bin/RNAeval
- bin/RNAfold
- bin/RNAforester
- bin/RNAheat
- bin/RNAinverse
- bin/RNAlocmin
- bin/RNAmultifold
- bin/RNApaln
- bin/RNAparconv
- bin/RNApdist
- bin/RNAplex
- bin/RNAplfold
- bin/RNAplot
- bin/RNApvmin
- bin/RNAsnoop
- bin/RNAsubopt
- bin/RNAup
- bin/RNAxplorer
- bin/b2ct
- bin/ct2db
- bin/kinwalker
- bin/popt
- include/ViennaRNA/2Dfold.h
- include/ViennaRNA/2Dpfold.h
- include/ViennaRNA/LPfold.h
- include/ViennaRNA/Lfold.h
- include/ViennaRNA/MEA.h
- include/ViennaRNA/PKplex.h
- include/ViennaRNA/PS_dot.h
- include/ViennaRNA/ProfileAln.h
- include/ViennaRNA/RNAstruct.h
- include/ViennaRNA/SHAPE.h
- include/ViennaRNA/ali_plex.h
- include/ViennaRNA/alifold.h
- include/ViennaRNA/aln_util.h
- include/ViennaRNA/alphabet.h
- include/ViennaRNA/backtrack/exterior.h
- include/ViennaRNA/backtrack/global.h
- include/ViennaRNA/backtrack/gquad.h
- include/ViennaRNA/backtrack/hairpin.h
- include/ViennaRNA/backtrack/internal.h
- include/ViennaRNA/backtrack/multibranch.h
- include/ViennaRNA/boltzmann_sampling.h
- include/ViennaRNA/centroid.h
- include/ViennaRNA/char_stream.h
- include/ViennaRNA/cofold.h
- include/ViennaRNA/combinatorics.h
- include/ViennaRNA/combinatorics/basic.h
- include/ViennaRNA/commands.h
- include/ViennaRNA/concentrations.h
- include/ViennaRNA/constraints.h
- include/ViennaRNA/constraints/SHAPE.h
- include/ViennaRNA/constraints/basic.h
- include/ViennaRNA/constraints/hard.h
- include/ViennaRNA/constraints/ligand.h
- include/ViennaRNA/constraints/soft.h
- include/ViennaRNA/constraints/soft_special.h
- include/ViennaRNA/constraints_SHAPE.h
- include/ViennaRNA/constraints_hard.h
- include/ViennaRNA/constraints_ligand.h
- include/ViennaRNA/constraints_soft.h
- include/ViennaRNA/convert_epars.h
- include/ViennaRNA/data/transform.h
- include/ViennaRNA/data_structures.h
- include/ViennaRNA/datastructures/array.h
- include/ViennaRNA/datastructures/basic.h
- include/ViennaRNA/datastructures/char_stream.h
- include/ViennaRNA/datastructures/dp_matrices.h
- include/ViennaRNA/datastructures/hash_tables.h
- include/ViennaRNA/datastructures/heap.h
- include/ViennaRNA/datastructures/lists.h
- include/ViennaRNA/datastructures/sparse_mx.h
- include/ViennaRNA/datastructures/stream_output.h
- include/ViennaRNA/datastructures/string.h
- include/ViennaRNA/dist_vars.h
- include/ViennaRNA/dp_matrices.h
- include/ViennaRNA/duplex.h
- include/ViennaRNA/edit_cost.h
- include/ViennaRNA/energy_const.h
- include/ViennaRNA/energy_par.h
- include/ViennaRNA/equilibrium_probs.h
- include/ViennaRNA/eval.h
- include/ViennaRNA/eval/basic.h
- include/ViennaRNA/eval/exterior.h
- include/ViennaRNA/eval/gquad.h
- include/ViennaRNA/eval/hairpin.h
The first 100 are listed.
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| ViennaRNA-2.7.2.tar.gz | 6.7253851e+07 | 1ab5f4a4f76fc85a2243546088e45f5d85f2d7a56cc656e969b005cce9bfab5f |
Master sites 1
- https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_7_x/
Commit history 0
No commits in the history this site was built from.