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Port details on branch 2022Q3
crux Software toolkit for phylogenetic inference
1.2.0_9 biology Deleted on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.2.0_9Version of this port present on the latest quarterly branch.
Broken BROKEN: No public distfiles
Deprecated DEPRECATED: Broken for more than 6 months
Expired This port expired on: 2018-06-06
Ignore 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 search for ports maintained by this maintainer
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/
Homepage    cgit ¦ GitHub ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (60 items)
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  1. /usr/local/share/licenses/crux-1.2.0_9/catalog.mk
  2. /usr/local/share/licenses/crux-1.2.0_9/LICENSE
  3. /usr/local/share/licenses/crux-1.2.0_9/BSD2CLAUSE
  4. /usr/local/share/licenses/crux-1.2.0_9/BSD3CLAUSE
  5. bin/crux
  6. bin/redpoint
  7. bin/MrRogers
  8. lib/Crux/lib/libCx.so
  9. lib/Crux/parsers/Fasta.log
  10. lib/Crux/parsers/Fasta.pickle
  11. lib/python2.7/site-packages/Crux/CTMatrix.so
  12. lib/python2.7/site-packages/Crux/Character.so
  13. lib/python2.7/site-packages/Crux/Config.py
  14. @rmtry lib/python2.7/site-packages/Crux/Config.pyo
  15. lib/python2.7/site-packages/Crux/Copying.py
  16. @rmtry lib/python2.7/site-packages/Crux/Copying.pyo
  17. lib/python2.7/site-packages/Crux/DistMatrix/Nj.so
  18. lib/python2.7/site-packages/Crux/DistMatrix/__init__.py
  19. lib/python2.7/site-packages/Crux/DistMatrix/__init__.so
  20. lib/python2.7/site-packages/Crux/Fasta.so
  21. lib/python2.7/site-packages/Crux/Mc3/Chain.so
  22. lib/python2.7/site-packages/Crux/Mc3/Post.so
  23. lib/python2.7/site-packages/Crux/Mc3/__init__.py
  24. lib/python2.7/site-packages/Crux/Mc3/__init__.so
  25. lib/python2.7/site-packages/Crux/Newick.so
  26. lib/python2.7/site-packages/Crux/Taxa.so
  27. lib/python2.7/site-packages/Crux/Tree/Bipart.so
  28. lib/python2.7/site-packages/Crux/Tree/Lik.so
  29. lib/python2.7/site-packages/Crux/Tree/Sumt.so
  30. lib/python2.7/site-packages/Crux/Tree/__init__.py
  31. lib/python2.7/site-packages/Crux/Tree/__init__.so
  32. lib/python2.7/site-packages/Crux/include/Crux/CTMatrix.pxd
  33. lib/python2.7/site-packages/Crux/include/Crux/Character.pxd
  34. lib/python2.7/site-packages/Crux/include/Crux/Crux/CxMath.pxd
  35. lib/python2.7/site-packages/Crux/include/Crux/Crux/CxMat.pxd
  36. lib/python2.7/site-packages/Crux/include/Crux/Crux/CxNewickLexer.pxd
  37. lib/python2.7/site-packages/Crux/include/Crux/Crux/CxRi.pxd
  38. lib/python2.7/site-packages/Crux/include/Crux/Crux/Cx.pxd
  39. lib/python2.7/site-packages/Crux/include/Crux/Crux/DistMatrix/CxDistMatrixLexer.pxd
  40. lib/python2.7/site-packages/Crux/include/Crux/Crux/Tree/CxLik.pxd
  41. lib/python2.7/site-packages/Crux/include/Crux/DistMatrix/Nj.pxd
  42. lib/python2.7/site-packages/Crux/include/Crux/DistMatrix/__init__.pxd
  43. lib/python2.7/site-packages/Crux/include/Crux/Fasta.pxd
  44. lib/python2.7/site-packages/Crux/include/Crux/Mc3/Chain.pxd
  45. lib/python2.7/site-packages/Crux/include/Crux/Mc3/Post.pxd
  46. lib/python2.7/site-packages/Crux/include/Crux/Mc3/__init__.pxd
  47. lib/python2.7/site-packages/Crux/include/Crux/Newick.pxd
  48. lib/python2.7/site-packages/Crux/include/Crux/SFMT/SFMT.pxd
  49. lib/python2.7/site-packages/Crux/include/Crux/Taxa.pxd
  50. lib/python2.7/site-packages/Crux/include/Crux/Tree/Bipart.pxd
  51. lib/python2.7/site-packages/Crux/include/Crux/Tree/Lik.pxd
  52. lib/python2.7/site-packages/Crux/include/Crux/Tree/Sumt.pxd
  53. lib/python2.7/site-packages/Crux/include/Crux/Tree/__init__.pxd
  54. lib/python2.7/site-packages/Crux/include/Crux/__init__.pxd
  55. lib/python2.7/site-packages/Crux/include/Crux/libc.pxd
  56. lib/python2.7/site-packages/Crux/include/Crux/libm.pxd
  57. lib/python2.7/site-packages/Crux/include/Parsing.pxd
  58. lib/python2.7/site-packages/Crux/__init__.py
  59. lib/python2.7/site-packages/Crux/__init__.so
  60. lib/python2.7/site-packages/Parsing.so
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Dependency lines:
  • crux>0:biology/crux
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
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Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gfortran6 : lang/gcc6
  2. gmake : devel/gmake
  3. python2.7 : lang/python27
  4. as : devel/binutils
Runtime dependencies:
  1. gfortran6 : lang/gcc6
  2. 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:
Expand this list (1 items)
Collapse this list.
  1. http://www.canonware.com/download/Crux/
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There are no commits on branch 2022Q3 for this port