BSD Ports

biology/infernal 1.1.5 FreeBSD

Search sequence databases for structural RNA homologs

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
License
BSD3CLAUSE
Categories
biology

Description

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.

In the other systems

SystemPortVersion
FreeBSDbiology/infernal1.1.5
DragonFlybiology/infernal1.1.5
HardenedBSDbiology/infernal1.1.5
GhostBSDbiology/infernal1.1.5

Install

Binary package:

pkg install infernal

From the ports tree:

cd /usr/ports/biology/infernal/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	infernal>0:biology/infernal

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest-1.1.5--1.1.5
FreeBSD:14:quarterly-1.1.5n/a-1.1.5
FreeBSD:15:latest-1.1.5n/a-1.1.5
FreeBSD:15:quarterly-1.1.5n/an/an/a
FreeBSD:16:latest-1.1.5n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

The Makefile names none itself; they come from USES and USE_*.

The full lists below include those, and their dependencies in turn.

Build dependencies 3

Configuration

Options name: biology_infernal

OptionDefaultDescription
DOCSoffBuild and/or install documentation
EXAMPLESoffBuild and/or install examples
TESToffBuild and/or run tests
USES
compiler:c11 gmake perl5 python:test shebangfix
Service scripts
none

Files

Manual pages 11
  • cmalign(1)
  • cmbuild(1)
  • cmcalibrate(1)
  • cmconvert(1)
  • cmemit(1)
  • cmfetch(1)
  • cmpress(1)
  • cmscan(1)
  • cmsearch(1)
  • cmstat(1)
  • infernal(1)
pkg-plist 46
  • bin/cmalign
  • bin/cmbuild
  • bin/cmcalibrate
  • bin/cmconvert
  • bin/cmemit
  • bin/cmfetch
  • bin/cmpress
  • bin/cmscan
  • bin/cmsearch
  • bin/cmstat
  • share/man/man1/cmalign.1.gz
  • share/man/man1/cmbuild.1.gz
  • share/man/man1/cmcalibrate.1.gz
  • share/man/man1/cmconvert.1.gz
  • share/man/man1/cmemit.1.gz
  • share/man/man1/cmfetch.1.gz
  • share/man/man1/cmpress.1.gz
  • share/man/man1/cmscan.1.gz
  • share/man/man1/cmsearch.1.gz
  • share/man/man1/cmstat.1.gz
  • share/man/man1/infernal.1.gz
  • share/doc/infernal/Userguide.pdf
  • share/examples/infernal/5S_rRNA.c.cm
  • share/examples/infernal/5S_rRNA.sto
  • share/examples/infernal/Cobalamin.c.cm
  • share/examples/infernal/Cobalamin.fa
  • share/examples/infernal/Cobalamin.sto
  • share/examples/infernal/Rfam.14.9.clanin
  • share/examples/infernal/metag-example.fa
  • share/examples/infernal/minifam-metag.out
  • share/examples/infernal/minifam.cm
  • share/examples/infernal/minifam.cm.i1f
  • share/examples/infernal/minifam.cm.i1i
  • share/examples/infernal/minifam.cm.i1m
  • share/examples/infernal/minifam.cm.i1p
  • share/examples/infernal/mrum-genome.fa
  • share/examples/infernal/mrum-tRNAs10.fa
  • share/examples/infernal/mrum-tRNAs10.out
  • share/examples/infernal/tRNA5-hand.c.cm
  • share/examples/infernal/tRNA5-hand.frag.sto
  • share/examples/infernal/tRNA5-hand.fraggiven.sto
  • share/examples/infernal/tRNA5-hand.sto
  • share/examples/infernal/tRNA5-mrum.out
  • share/examples/infernal/tRNA5-noss.sto
  • share/examples/infernal/tRNA5.c.cm
  • share/examples/infernal/tRNA5.sto
distinfo 1
FileSizeSHA256
infernal-1.1.5.tar.gz3.1300142e+07ad4ddae02f924ca7c85bc8c4a79c9f875af8df96aeb726702fa985cbe752497f
Master sites 1
  • http://eddylab.org/infernal/

Commit history 0

No commits in the history this site was built from.