BSD Portsbiology/hmmer 3.4 FreeBSD
Profile hidden Markov models for biological sequence analysis
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
7bed7b09f6- License
- BSD3CLAUSE
- Categories
- biology
- Package size
- 2102.2 KiB, 13519.6 KiB installed
Description
HMMER is an implementation of profile hidden Markov model methods for sensitive searches of biological sequence databases using multiple sequence alignments as queries.
Given a multiple sequence alignment as input, HMMER builds a statistical model called a "hidden Markov model" which can then be used as a query into a sequence database to find (and/or align) additional homologues of the sequence family.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/hmmer | 3.4 |
| OpenBSD | biology/hmmer | 3.1beta2p0 |
| NetBSD | biology/hmmer | 3.0nb1 |
| DragonFly | biology/hmmer | 3.4 |
| HardenedBSD | biology/hmmer | 3.4 |
| GhostBSD | biology/hmmer | 3.4 |
Install
Binary package:
pkg install hmmerFrom the ports tree:
cd /usr/ports/biology/hmmer/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= hmmer>0:biology/hmmerPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 3.4 | 3.4 | - | 3.4 | 3.4 |
| FreeBSD:14:quarterly | 3.4 | 3.4 | n/a | 3.4 | 3.4 |
| FreeBSD:15:latest | 3.4 | 3.4 | n/a | 3.4 | 3.4 |
| FreeBSD:15:quarterly | 3.4 | 3.4 | n/a | n/a | n/a |
| FreeBSD:16:latest | 3.4 | 3.4 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/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
No port depends on this one.
Configuration
Options name: biology_hmmer
| Option | Default | Description |
|---|---|---|
| DOCS | off | Build and/or install documentation |
| EXAMPLES | off | Build and/or install examples |
| TEST | off | Build and/or run tests |
- USES
- compiler:c11 gmake perl5 python:test shebangfix
- Service scripts
- none
Message after installing
HMMER reads three optional environment variables: HMMERDB - directory location of HMM databases (e.g. PFAM) BLASTDB - directory location of FASTA-formatted sequence databases BLASTMAT - directory location of PAM scoring matrices The BLASTDB and BLASTMAT variables are shared with versions of BLAST such as NCBI BLAST 2.0 (contained in the biology/ncbi-toolkit port). If these variables are set, you do not have to specify the full path to your databases on the command line when using HMMER. Please see the documentation for more information.
Files
Manual pages 20
- alimask(1)
- hmmalign(1)
- hmmbuild(1)
- hmmconvert(1)
- hmmemit(1)
- hmmer(1)
- hmmfetch(1)
- hmmlogo(1)
- hmmpgmd(1)
- hmmpgmd_shard(1)
- hmmpress(1)
- hmmscan(1)
- hmmsearch(1)
- hmmsim(1)
- hmmstat(1)
- jackhmmer(1)
- makehmmerdb(1)
- nhmmer(1)
- nhmmscan(1)
- phmmer(1)
pkg-plist 52
- bin/alimask
- bin/hmmalign
- bin/hmmbuild
- bin/hmmconvert
- bin/hmmemit
- bin/hmmfetch
- bin/hmmlogo
- bin/hmmpgmd
- bin/hmmpgmd_shard
- bin/hmmpress
- bin/hmmscan
- bin/hmmsearch
- bin/hmmsim
- bin/hmmstat
- bin/jackhmmer
- bin/makehmmerdb
- bin/nhmmer
- bin/nhmmscan
- bin/phmmer
- share/man/man1/alimask.1.gz
- share/man/man1/hmmalign.1.gz
- share/man/man1/hmmbuild.1.gz
- share/man/man1/hmmconvert.1.gz
- share/man/man1/hmmemit.1.gz
- share/man/man1/hmmer.1.gz
- share/man/man1/hmmfetch.1.gz
- share/man/man1/hmmlogo.1.gz
- share/man/man1/hmmpgmd.1.gz
- share/man/man1/hmmpgmd_shard.1.gz
- share/man/man1/hmmpress.1.gz
- share/man/man1/hmmscan.1.gz
- share/man/man1/hmmsearch.1.gz
- share/man/man1/hmmsim.1.gz
- share/man/man1/hmmstat.1.gz
- share/man/man1/jackhmmer.1.gz
- share/man/man1/makehmmerdb.1.gz
- share/man/man1/nhmmer.1.gz
- share/man/man1/nhmmscan.1.gz
- share/man/man1/phmmer.1.gz
- share/doc/hmmer/Userguide.pdf
- share/examples/hmmer/7LESS_DROME
- share/examples/hmmer/HBB_HUMAN
- share/examples/hmmer/MADE1.hmm
- share/examples/hmmer/MADE1.sto
- share/examples/hmmer/Pkinase.hmm
- share/examples/hmmer/Pkinase.sto
- share/examples/hmmer/dna_target.fa
- share/examples/hmmer/fn3.hmm
- share/examples/hmmer/fn3.sto
- share/examples/hmmer/globins4.hmm
- share/examples/hmmer/globins4.sto
- share/examples/hmmer/globins45.fa
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| hmmer-3.4.tar.gz | 1.9669667e+07 | ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3 |
Master sites 1
- http://eddylab.org/software/hmmer/