| Port details on branch 2022Q3 |
- hmmer Profile hidden Markov models for biological sequence analysis
- 3.3.2_1 biology
 =0      3.3.2_1Version of this port present on the latest quarterly branch. - Maintainer: mzaki@e-mail.ne.jp
- Port Added: unknown
- Last Update: 2024-02-22 13:23:46
- Commit Hash: c080051
- License: BSD3CLAUSE
- WWW:
- http://hmmer.org/
- 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.
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- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/hmmer/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/hmmer
- pkg install hmmer
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: hmmer
- Flavors: there is no flavor information for this port.
- ONLY_FOR_ARCHS: amd64 i386 powerpc powerpc64
- distinfo:
- TIMESTAMP = 1665491511
SHA256 (hmmer-3.3.2.tar.gz) = 92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69
SIZE (hmmer-3.3.2.tar.gz) = 18213049
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- gmake>=4.3 : devel/gmake
- Test dependencies:
-
- python3.9 : lang/python39
- perl5>=5.36<5.37 : lang/perl5.36
- This port is required by:
- for Run
-
- biology/barrnap
Configuration Options:- ===> The following configuration options are available for hmmer-3.3.2_1:
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
- Options name:
- biology_hmmer
- USES:
- compiler:c11 gmake perl5 python:test shebangfix
- pkg-message:
- For install:
- 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.
- Master Sites:
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