BSD Portsbiology/hhsuite 3.3.0_3 FreeBSD
Remote protein homology detection suite
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
0b23c55e5d- License
- GPLv3
- Categories
- biology, science
- Package size
- 7660.6 KiB, 116894.2 KiB installed
Description
SIMD-vectorized implementation of the Viterbi algorithm for profile HMM alignment and introduced various other speed-ups. This accelerated HHsearch by a factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is ~10x faster than PSI-BLAST and ~20x faster than HMMER3. Jobs to perform HHsearch and HHblits searches with many query profile HMMs can be parallelized over cores and over servers in a cluster using OpenMP and message passing interface (MPI).
In the other systems
The newest version among them is 3.3.0, as upstream numbers it.
| System | Port | Version | Vulnerabilities | Status | Maintainer | Last update |
|---|---|---|---|---|---|---|
| FreeBSD | biology/hhsuite | 3.3.0_3 newest | none known | - | [email protected] | 2026-10-05 |
| HardenedBSD | biology/hhsuite | 3.3.0_3 newest | no data | - | [email protected] | - |
| GhostBSD | biology/hhsuite | 3.3.0_3 newest | no data | - | [email protected] | - |
Install
Binary package:
pkg install hhsuiteFrom the ports tree:
cd /usr/ports/biology/hhsuite/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= hhsuite>0:biology/hhsuitePackages
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 | 3.3.0_3 | 3.3.0_3 | - | - | - |
| FreeBSD:14:quarterly | 3.3.0_3 | 3.3.0_3 | n/a | - | - |
| FreeBSD:15:latest | 3.3.0_3 | 3.3.0_3 | n/a | - | - |
| FreeBSD:15:quarterly | 3.3.0_3 | 3.3.0_3 | n/a | n/a | n/a |
| FreeBSD:16:latest | 3.3.0_3 | 3.3.0_3 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Library 1
libmpi.so: net/openmpi
The full lists below include those, and their dependencies in turn.
Build dependencies 36
- archivers/liblz4
- archivers/zlib-ng
- archivers/zstd
- devel/binutils
- devel/cmake-core
- devel/gettext-runtime
- devel/hwloc2
- devel/jsoncpp
- devel/level-zero
- devel/libevent
- devel/libffi
- devel/libpciaccess
- devel/libunistring
- devel/libuv
- devel/ninja
- devel/readline
- dns/libidn2
- lang/gcc14
- lang/perl5.42
- lang/python312
- math/gmp
- math/mpc
- math/mpdecimal
- math/mpfr
- misc/hwdata
- net/openmpi
- net/pmix
- net/prrte
- ports-mgmt/pkg
- print/indexinfo
- security/libgcrypt
- security/libgpg-error
- security/munge
- security/rhash
- textproc/expat2
- textproc/libxml2
Run dependencies 28
- archivers/liblz4
- archivers/zlib-ng
- archivers/zstd
- devel/binutils
- devel/gettext-runtime
- devel/hwloc2
- devel/level-zero
- devel/libevent
- devel/libffi
- devel/libpciaccess
- devel/readline
- lang/gcc14
- lang/perl5.42
- lang/python312
- math/gmp
- math/mpc
- math/mpdecimal
- math/mpfr
- misc/hwdata
- net/openmpi
- net/pmix
- net/prrte
- print/indexinfo
- security/libgcrypt
- security/libgpg-error
- security/munge
- textproc/expat2
- textproc/libxml2
No port depends on this one.
Configuration
No options to configure.
- USES
- compiler:c++11-lang cmake perl5 python shebangfix
- Service scripts
- none
Files
pkg-plist 59
- bin/a3m_database_extract
- bin/a3m_database_filter
- bin/a3m_database_reduce
- bin/a3m_extract
- bin/a3m_reduce
- bin/cstranslate
- bin/cstranslate_mpi
- bin/ffindex_apply
- bin/ffindex_apply_mpi
- bin/ffindex_build
- bin/ffindex_from_fasta
- bin/ffindex_from_fasta_with_split
- bin/ffindex_get
- bin/ffindex_modify
- bin/ffindex_order
- bin/ffindex_reduce
- bin/ffindex_unpack
- bin/hhalign
- bin/hhalign_mpi
- bin/hhalign_omp
- bin/hhblits
- bin/hhblits_ca3m
- bin/hhblits_mpi
- bin/hhblits_omp
- bin/hhconsensus
- bin/hhfilter
- bin/hhmake
- bin/hhsearch
- bin/hhsearch_mpi
- bin/hhsearch_omp
- share/hhsuite/data/context_data.crf
- share/hhsuite/data/context_data.lib
- share/hhsuite/data/cs219.lib
- share/hhsuite/data/do_not_delete
- share/hhsuite/data/do_not_delete.phr
- share/hhsuite/data/do_not_delete.pin
- share/hhsuite/data/do_not_delete.psq
- share/hhsuite/scripts/Align.pm
- share/hhsuite/scripts/HHPaths.pm
- share/hhsuite/scripts/a3m.py
- share/hhsuite/scripts/addss.pl
- share/hhsuite/scripts/check_a3m.py
- share/hhsuite/scripts/cif2fasta.py
- share/hhsuite/scripts/create_profile_from_hhm.pl
- share/hhsuite/scripts/create_profile_from_hmmer.pl
- share/hhsuite/scripts/ffindex.py
- share/hhsuite/scripts/get_a3m_size.py
- share/hhsuite/scripts/hh_reader.py
- share/hhsuite/scripts/hhmakemodel.pl
- share/hhsuite/scripts/hhmakemodel.py
- share/hhsuite/scripts/hhsuitedb.py
- share/hhsuite/scripts/mergeali.pl
- share/hhsuite/scripts/multithread.pl
- share/hhsuite/scripts/pdb2fasta.pl
- share/hhsuite/scripts/pdbfilter.pl
- share/hhsuite/scripts/pdbfilter.py
- share/hhsuite/scripts/reformat.pl
- share/hhsuite/scripts/renumberpdb.pl
- share/hhsuite/scripts/splitfasta.pl
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| soedinglab-hh-suite-v3.3.0_GH0.tar.gz | 6.490149e+06 | dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964 |