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Port details
infernal Search sequence databases for structural RNA homologs
1.1.2 biology 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
Maintainer: mzaki@niid.go.jp search for ports maintained by this maintainer
Port Added: 2018-06-06 15:15:35
Last Update: 2018-09-28 00:02:56
SVN Revision: 480834
License: BSD3CLAUSE
Infernal, standing for "INFERence of RNA ALignment", is a tool for searching
DNA sequence database for RNA structure and sequence similarities.

It is based on Covariance Model (CM), which scores a combination of sequence
consensus and RNA secondary structure consensus, and thus is more capable of
identifying RNA homologs than using primary sequence profile.

The Rfam database of RNA families is based on Infernal. 

Citation:
Nawrocki & Eddy (2013) Infernal 1.1: 100-fold faster RNA homology searches,
Bioinformatics 29: 2933-2935.

WWW: http://eddylab.org/infernal/
SVNWeb : Homepage
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (46 items)
  1. /usr/local/share/licenses/infernal-1.1.2/catalog.mk
  2. /usr/local/share/licenses/infernal-1.1.2/LICENSE
  3. /usr/local/share/licenses/infernal-1.1.2/BSD3CLAUSE
  4. bin/cmalign
  5. bin/cmbuild
  6. bin/cmcalibrate
  7. bin/cmconvert
  8. bin/cmemit
  9. bin/cmfetch
  10. bin/cmpress
  11. bin/cmscan
  12. bin/cmsearch
  13. bin/cmstat
  14. man/man1/cmalign.1.gz
  15. man/man1/cmbuild.1.gz
  16. man/man1/cmcalibrate.1.gz
  17. man/man1/cmconvert.1.gz
  18. man/man1/cmemit.1.gz
  19. man/man1/cmfetch.1.gz
  20. man/man1/cmpress.1.gz
  21. man/man1/cmscan.1.gz
  22. man/man1/cmsearch.1.gz
  23. man/man1/cmstat.1.gz
  24. man/man1/infernal.1.gz
  25. share/doc/infernal/Userguide.pdf
  26. share/examples/infernal/5S_rRNA.c.cm
  27. share/examples/infernal/5S_rRNA.sto
  28. share/examples/infernal/Cobalamin.c.cm
  29. share/examples/infernal/Cobalamin.fa
  30. share/examples/infernal/Cobalamin.sto
  31. share/examples/infernal/metag-example.fa
  32. share/examples/infernal/minifam-metag.out
  33. share/examples/infernal/minifam.cm
  34. share/examples/infernal/minifam.cm.i1f
  35. share/examples/infernal/minifam.cm.i1i
  36. share/examples/infernal/minifam.cm.i1m
  37. share/examples/infernal/minifam.cm.i1p
  38. share/examples/infernal/mrum-genome.fa
  39. share/examples/infernal/mrum-tRNAs10.fa
  40. share/examples/infernal/mrum-tRNAs10.out
  41. share/examples/infernal/tRNA5-hand.c.cm
  42. share/examples/infernal/tRNA5-hand.sto
  43. share/examples/infernal/tRNA5-mrum.out
  44. share/examples/infernal/tRNA5-noss.sto
  45. share/examples/infernal/tRNA5.c.cm
  46. share/examples/infernal/tRNA5.sto
  47. Collapse this list.
Dependency lines:
  • infernal>0:biology/infernal

To install the port: cd /usr/ports/biology/infernal/ && make install clean
To add the package: pkg install infernal

PKGNAME: infernal

There is no flavor information for this port.

ONLY_FOR_ARCHS: amd64 i386 powerpc64

distinfo:

TIMESTAMP = 1528251928
SHA256 (infernal-1.1.2.tar.gz) = ac8c24f484205cfb7124c38d6dc638a28f2b9035b9433efec5dc753c7e84226b
SIZE (infernal-1.1.2.tar.gz) = 19364073


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. gmake : devel/gmake

This port is required by:

for Run * - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...
Configuration Options
===> The following configuration options are available for infernal-1.1.2:
     DOCS=on: Build and/or install documentation
     EXAMPLES=on: Build and/or install examples
     TEST=off: Build and/or run tests
===> Use 'make config' to modify these settings

USES:
gmake

Master Sites:
  1. http://eddylab.org/infernal/

Number of commits found: 2

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
27 Sep 2018 23:02:56
Original commit files touched by this commit  1.1.2
Revision:480834
linimon search for other commits by this committer
Allow building on powerpc64.

PR:		231759
Submitted by:	Piotr Kubaj
Approved by:	portmgr (tier-2 blanket)
06 Jun 2018 15:15:18
Original commit files touched by this commit  1.1.2
Revision:471850
krion search for other commits by this committer
Add new port: biology/infernal

Infernal is a tool for searching DNA sequence database for RNA
structure and sequence similarities. The Rfam database of RNA
families is based on Infernal, and we can search DNA sequences for
structural homologs of Rfam families.

WWW: http://eddylab.org/infernal/

PR:		228776
Submitted by:	Motomichi Matsuzaki <mzaki@niid.go.jp>

Number of commits found: 2

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