| Port details on branch 2022Q2 |
- viennarna Alignment tools for the structural analysis of RNA
- 2.6.4_2 biology
 =0      2.6.4_2Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2019-06-24 09:29:23
- Last Update: 2024-03-02 20:35:56
- Commit Hash: 5ebea8e
- License: ViennaRNALicense
- WWW:
- https://www.tbi.univie.ac.at/RNA/
- 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).
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- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- viennarna>0:biology/viennarna
- Conflicts:
- CONFLICTS_INSTALL:
- Conflicts Matches:
-
There are no Conflicts Matches for this port. This is usually an error.
- To install the port:
- cd /usr/ports/biology/viennarna/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/viennarna
- pkg install viennarna
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: viennarna
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1699041043
SHA256 (ViennaRNA-2.6.4.tar.gz) = d1259ce5809601a12b0dc9b724ea2c55806fece80d8d83ad417ea8a2dd574982
SIZE (ViennaRNA-2.6.4.tar.gz) = 69749819
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- bash : shells/bash
- lapacke>0 : math/lapacke
- libgd>0 : graphics/gd
- swig : devel/swig
- xxd : sysutils/xxd
- bison : devel/bison
- gfortran13 : lang/gcc13
- gmake>=4.3 : devel/gmake
- pkgconf>=1.3.0_1 : devel/pkgconf
- as : devel/binutils
- autoconf>=2.71 : devel/autoconf
- automake>=1.16.5 : devel/automake
- libtoolize : devel/libtool
- perl5>=5.36<5.37 : lang/perl5.36
- ice.pc : x11/libICE
- x11.pc : x11/libX11
- xext.pc : x11/libXext
- Runtime dependencies:
-
- gfortran13 : lang/gcc13
- perl5>=5.36<5.37 : lang/perl5.36
- ice.pc : x11/libICE
- x11.pc : x11/libX11
- xext.pc : x11/libXext
- indexinfo : print/indexinfo
- Library dependencies:
-
- libgmp.so : math/gmp
- libgsl.so : math/gsl
- liblapack.so : math/lapack
- libmpfr.so : math/mpfr
- This port is required by:
- for Build
-
- biology/locarna
Configuration Options:- ===> The following configuration options are available for viennarna-2.6.4_2:
DOCS=on: Build and/or install documentation
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
- Options name:
- biology_viennarna
- USES:
- autoreconf bison compiler:c++17-lang fortran gmake libtool localbase perl5 pkgconfig xorg
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
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