BSD Portsbiology/hmmer 3.4 DragonFly
Profile hidden Markov models for biological sequence analysis
- System
- DragonFly
- Repository
- DPorts
- Maintainer
- [email protected] (as in FreeBSD)
- License
- BSD3CLAUSE
- Categories
- biology
- Package size
- 1969.4 KiB, 13580.1 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
The newest version among them is 3.4, as upstream numbers it.
| System | Port | Version | Vulnerabilities | Status | Maintainer | Last update |
|---|---|---|---|---|---|---|
| DragonFly | biology/hmmer | 3.4 newest | none known | - | [email protected] | - |
| FreeBSD | biology/hmmer | 3.4 newest | none known | - | [email protected] | 2026-10-15 |
| OpenBSD | biology/hmmer | 3.1beta2p0 | no data | - | Senthil Kumar M <[email protected]> | - |
| NetBSD | biology/hmmer | 3.0nb1 | none known | - | [email protected] | - |
| HardenedBSD | biology/hmmer | 3.4 newest | no data | - | [email protected] | - |
| GhostBSD | biology/hmmer | 3.4 newest | no data | - | [email protected] | - |
Install
Binary package:
pkg install hmmerFrom DPorts:
cd /usr/dports/biology/hmmer && make install cleanDependency graph
Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.
Dependencies
Required by 1
Configuration
No options to configure.
- 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.