Port details on branch 2022Q3 |
- crux Software toolkit for phylogenetic inference
- 1.2.0_9 biology
=0 1.2.0_9Version of this port present on the latest quarterly branch.
- BROKEN: No public distfiles
DEPRECATED: Broken for more than 6 months This port expired on: 2018-06-06 IGNORE: is marked as broken: No public distfiles
- There is no maintainer for this port.
- Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org
- Port Added: 2009-06-08 23:51:06
- Last Update: 2018-06-07 00:34:18
- SVN Revision: 471892
- Also Listed In: python
- License: BSD2CLAUSE BSD3CLAUSE
- WWW:
- http://www.canonware.com/Crux/
- Description:
- Crux is a software toolkit for molecular phylogenetic inference. It is
structured as a set of Python modules, which makes it possible to quickly
develop Python scripts that perform unique, non-canned analyses. Features
include:
* Tree log-likelihoods can be computed under a variety of models,
including all specializations of GTR+I+G and mixture models. Tree
likelihoods can be computed in parallel via pthreads.
* Bayesian Markov chain Monte Carlo (MCMC) methods (with Metropolis
coupling) can sample among non-nested models using reversible model
jumps.
* Crux is capable of simulating character data under any model its
likelihood engine is capable of.
* The neighbor joining (NJ) and relaxed neighbor joining (RNJ)
implementations are among the fastest in existence.
* Pairwise distances between sequences can be computed based on percent
identity, or using methods that correct for multiple hits
(Jukes-Cantor, Kimura, and logDet).
WWW: http://www.canonware.com/Crux/
-
cgit ¦ GitHub ¦ GitHub ¦ GitLab ¦
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- No installation instructions:
- This port has been deleted.
- PKGNAME: crux
- Flavors: there is no flavor information for this port.
- distinfo:
- SHA256 (crux-1.2.0.tar.bz2) = 11f677e8bf62db69e75271670ea50fb5a23c8a2c526fa9d16ccf2e736e5212c5
SIZE (crux-1.2.0.tar.bz2) = 1187274
No package information for this port in our database- Sometimes this happens. Not all ports have packages.
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- gfortran6 : lang/gcc6
- gmake : devel/gmake
- python2.7 : lang/python27
- as : devel/binutils
- Runtime dependencies:
-
- gfortran6 : lang/gcc6
- python2.7 : lang/python27
- There are no ports dependent upon this port
Configuration Options:
- ===> The following configuration options are available for crux-1.2.0_9:
SYS_LINALG=off: Enable system ATLAS/LAPACK
===> Use 'make config' to modify these settings
- Options name:
- N/A
- USES:
- fortran gmake python tar:bzip2
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
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