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Category listing - biology
Software related to biology. - Number of ports in this category): 270

Ports marked with a * actually reside within another category but have biology listed as a secondary category.

py-orange3-bioinformatics Orange add-on providing common functionality for bioinformatics
4.8.4_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 4.8.4_1Version of this port present on the latest quarterly branch.
Deprecated DEPRECATED: Depends on expiring misc/orange3
Expiration Date EXPIRATION DATE: 2025-06-21
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-06-14 06:26:12
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: python
License: GPLv3
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}orange3-bioinformatics>0:biology/py-orange3-bioinformatics@${PY_FLAVOR}
py-orange3-single-cell Orange add-on for gene expression of single cell data
0.8.2_6 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.8.2_6Version of this port present on the latest quarterly branch.
Deprecated DEPRECATED: Depends on expired math/py-fastdtw and expiring misc/orange3
Expiration Date EXPIRATION DATE: 2025-06-21
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-08-07 07:50:53
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: python
License: AGPLv3+
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}orange3-single-cell>0:biology/py-orange3-single-cell@${PY_FLAVOR}
py-pandas-charm Library for getting character matrices into and out of pandas
0.3.0_3 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.3.0_3Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2020-05-16 00:14:20
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: python
License: MIT
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}pandas-charm>0:biology/py-pandas-charm@${PY_FLAVOR}
py-py2bit Python interface for 2bit packed nucleotide files
0.3.0_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.3.0_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-10-13 12:57:10
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: python
License: MIT
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}py2bit>0:biology/py-py2bit@${PY_FLAVOR}
py-pybigwig Python access to bigWig files using libBigWig
0.3.22_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.3.22_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-10-13 13:09:05
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: python
License: MIT
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}pyBigWig>0:biology/py-pybigwig@${PY_FLAVOR}
py-pyfaidx Efficient pythonic random access to fasta subsequences
0.5.9.5_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.5.9.5_1Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-10-19 02:05:49
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: python
License: BSD3CLAUSE
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}pyfaidx>0:biology/py-pyfaidx@${PY_FLAVOR}
py-pymol OpenGL-based molecular visualization system
3.0.0_1* search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 3.0.0_1Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-12-19 19:49:25
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: python science
License: PyMOL
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}pymol>0:science/py-pymol@${PY_FLAVOR}
py-pyrodigal Python binding for Prodigal, an ORF finder for genomes and metagenomes
3.6.3 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 3.6.3Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2022-12-06 17:27:05
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: python
License: GPLv3
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}pyrodigal>0:biology/py-pyrodigal@${PY_FLAVOR}
py-pysam Python module for reading, manipulating and writing genomic data sets
0.23.0_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.23.0_1Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-05-06 06:30:42
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: python
License: MIT
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR}
py-python-libsbml LibSBML Python API
5.20.4_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 5.20.4_1Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-08-17 21:33:06
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: python
License: LGPL21
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}python-libsbml>0:biology/py-python-libsbml@${PY_FLAVOR}
py-pywgsim Modified wgsim genomic data simulator
0.5.2_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.5.2_2Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-09-06 12:57:08
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: python
License: MIT
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}pywgsim>0:biology/py-pywgsim@${PY_FLAVOR}
py-resdk Resolwe SDK to interact with Resolwe server and Resolwe Bioinformatics
22.0.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 21.2.1Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-04-20 04:24:12
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: python
License: APACHE20
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}resdk>0:biology/py-resdk@${PY_FLAVOR}
py-scikit-bio Data structures, algorithms, educational resources for bioinformatics
0.6.3 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.6.3Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2020-05-16 02:25:40
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: education python
License: BSD3CLAUSE
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}scikit-bio>0:biology/py-scikit-bio@${PY_FLAVOR}
py-valerius Python bioinformatics tools
0.2_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.2_1Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2022-10-04 04:09:26
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: python
License: MIT
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}valerius>0:biology/py-valerius@${PY_FLAVOR}
py-xenaPython API for Xena Hub to access genetic information shared through the hub
1.0.14_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.0.14_1Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-04-12 17:01:25
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: python
License: APACHE20
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}xenaPython>0:biology/py-xenaPython@${PY_FLAVOR}
pyfasta Fast, memory-efficient, pythonic access to fasta sequence files
0.5.2_6 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.5.2_6Version of this port present on the latest quarterly branch.
Maintainer: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2009-11-18 05:53:48
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: python
License: MIT
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}pyfasta>0:biology/pyfasta@${PY_FLAVOR}
python-nexus Generic nexus file format reader for python
2.9.0_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.9.0_1Version of this port present on the latest quarterly branch.
Maintainer: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2009-12-29 13:39:49
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: python
License: BSD3CLAUSE
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}python-nexus>0:biology/python-nexus@${PY_FLAVOR}
rainbow Efficient clustering and assembling of short reads, especially for RAD
2.0.4 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.0.4Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-02 16:50:56
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
License: GPLv3+
Dependency lines:
  • rainbow>0:biology/rainbow
rampler Standalone module for sampling genomic sequences
2.0.0_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.0.0_1Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-01-19 09:50:02
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
License: MIT
Dependency lines:
  • rampler>0:biology/rampler
raster3d Set of tools for generating raster images of proteins and molecules
3.0.7_5* search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 3.0.7_5Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2006-04-28 14:21:11
People watching this port, also watch:: slrn, aalib, xcircuit, p5-File-Tail, fcgi-devkit
Also Listed In: graphics
License: ART20
Dependency lines:
  • raster3d>0:graphics/raster3d
readseq Read and reformat biosequences, Java command-line version
2.1.19 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.1.19Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-04-18 13:54:12
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: java
License: PD
Dependency lines:
  • readseq>0:biology/readseq
rna-seq Metaport for RNA-Seq analysis
0.1.4 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.1.4Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2022-12-14 00:00:51
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: python
License: NA
Dependency lines:
  • rna-seq>0:biology/rna-seq
ruby-bio Integrated environment for Bioinformatics written in Ruby
1.5.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.5.1Version of this port present on the latest quarterly branch.
Maintainer: mauricio@arareko.net search for ports maintained by this maintainer
Port Added: 2001-10-24 03:21:52
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: ruby
License: GPLv2 RUBY
Dependency lines:
  • ruby30-bio>0:biology/ruby-bio
rubygem-bio Integrated environment for Bioinformatics written in Ruby
2.0.6 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.0.6Version of this port present on the latest quarterly branch.
Maintainer: ruby@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-02-05 04:27:03
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: rubygems
License: BSD2CLAUSE RUBY
Dependency lines:
  • rubygem-bio>0:biology/rubygem-bio
rubygem-bio-executables Collection of miscellaneous utilities for bioinformatics
1.0.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.0.0Version of this port present on the latest quarterly branch.
Maintainer: sunpoet@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2020-07-24 07:10:30
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: rubygems
License: BSD2CLAUSE RUBY
Dependency lines:
  • rubygem-bio-executables>0:biology/rubygem-bio-executables
rubygem-bio-old-biofetch-emulator Emulate Bio::Fetch object
1.0.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.0.0Version of this port present on the latest quarterly branch.
Maintainer: sunpoet@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2020-07-24 07:10:45
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: rubygems
License: MIT
Dependency lines:
  • rubygem-bio-old-biofetch-emulator>0:biology/rubygem-bio-old-biofetch-emulator
rubygem-bio-shell Command-line interface on BioRuby
1.0.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.0.1Version of this port present on the latest quarterly branch.
Maintainer: sunpoet@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2020-07-24 07:11:01
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: rubygems
License: BSD2CLAUSE RUBY
Dependency lines:
  • rubygem-bio-shell>0:biology/rubygem-bio-shell
salmon Transcript-level quantification of RNA-seq from lightweight alignments
1.10.2_8 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.10.2_7Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2023-07-21 23:09:07
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
License: GPLv3
Dependency lines:
  • salmon>0:biology/salmon
sam2pairwise Show pairwise alignment for each read in a SAM file
1.0.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.0.0Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-09-07 20:36:08
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License: MIT
Dependency lines:
  • sam2pairwise>0:biology/sam2pairwise
samtools Tools for manipulating next-generation sequencing data
1.21 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.21Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2014-12-15 21:59:37
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License: MIT
Dependency lines:
  • samtools>0:biology/samtools
scrm Coalescent simulator for biological sequences
1.7.4_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.7.4_1Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2020-05-15 04:58:32
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License: GPLv3
Dependency lines:
  • scrm>0:biology/scrm
seaview Multiple DNA/protein sequence alignment editor
5.1,1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 5.1,1Version of this port present on the latest quarterly branch.
Maintainer: bofh@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
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License: GPLv3
Dependency lines:
  • seaview>0:biology/seaview
seqan C++ sequence analysis template library
2.4.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.4.0Version of this port present on the latest quarterly branch.
Maintainer: h2+fbsdports@fsfe.org search for ports maintained by this maintainer
Port Added: 2012-06-06 17:52:27
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License: BSD3CLAUSE
Dependency lines:
  • seqan>0:biology/seqan
seqan-apps Official bioinformatic applications based on the SeqAn library
2.4.0_11 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.4.0_11Version of this port present on the latest quarterly branch.
Maintainer: h2+fbsdports@fsfe.org search for ports maintained by this maintainer
Port Added: 2016-05-10 00:52:12
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License: BSD3CLAUSE LGPL3 GPLv3
Dependency lines:
  • seqan-apps>0:biology/seqan-apps
seqan1 C++ Sequence Analysis Library
1.3.1_4 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.3.1_4Version of this port present on the latest quarterly branch.
Maintainer: h2+fbsdports@fsfe.org search for ports maintained by this maintainer
Port Added: 2016-05-10 01:05:34
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License: BSD3CLAUSE
Dependency lines:
  • seqan1>0:biology/seqan1
seqan3 C++ header-only library for biological sequence analysis
3.3.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 3.3.0Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-05-12 01:24:05
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Also Listed In: devel math
License: BSD3CLAUSE
Dependency lines:
  • seqan3>0:biology/seqan3
seqkit Cross-platform and ultrafast toolkit for FASTA/Q file manipulation
2.10.0_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.10.0Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-04-16 21:06:12
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License: MIT
Dependency lines:
  • seqkit>0:biology/seqkit
seqtk Tool for processing sequences in FASTA/FASTQ format
1.4 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.4Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-03 20:57:19
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License: GPLv2
Dependency lines:
  • seqtk>0:biology/seqtk
seqwish Alignment to variation graph inducer
0.7.11_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.7.11_1Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2023-07-21 21:42:05
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License: MIT
Dependency lines:
  • seqwish>0:biology/seqwish
sigviewer Viewing application for biosignals
0.6.4.13_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.6.4.13_2Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-08-17 07:06:07
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License: GPLv3
Dependency lines:
  • sigviewer>0:biology/sigviewer
simbody Multibody dynamics library for (bio)mechanical systems simulation
3.7_8* search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 3.7_8Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-11-15 06:47:08
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Also Listed In: science
License: APACHE20
Dependency lines:
  • simbody>0:science/simbody
slclust Single-linkage clustering with Jaccard similarity
2010.02.02 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2010.02.02Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2016-03-23 11:00:52
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License: ART10
Dependency lines:
  • slclust>0:biology/slclust
smithwaterman Smith-waterman-gotoh alignment algorithm
g20160702 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout g20160702Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-15 17:46:20
People watching this port, also watch:: urbackup-server, py311-Automat, py311-python-gdsii, py311-PyOpenGL, jdictionary
License: GPLv2
Dependency lines:
  • smithwaterman>0:biology/smithwaterman
snpeff Genetic variant annotation and effect prediction toolbox
5.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 5.1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-04-18 18:48:08
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Also Listed In: java python
License: MIT
Dependency lines:
  • snpeff>0:biology/snpeff
spoa C++ implementation of the partial order alignment (POA) algorithm
4.1.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 4.1.0Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-01-19 09:28:06
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License: MIT
Dependency lines:
  • spoa>0:biology/spoa
sra-tools NCBI's toolkit for handling data in INSDC Sequence Read Archives
3.2.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 3.2.1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-06-22 18:00:14
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Also Listed In: java
License: PD LGPL21+
Dependency lines:
  • sra-tools>0:biology/sra-tools
stacks Software pipeline for building loci from short-read sequences
2.68 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.68Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-03-31 13:16:34
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: perl5 python
License: GPLv2
Dependency lines:
  • stacks>0:biology/stacks
star Spliced Transcripts Alignment to a Reference
2.7.11.a_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.7.11.a_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-04-21 20:31:13
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
License: GPLv3
Dependency lines:
  • rna-STAR>0:biology/star
stringtie Transcript assembly and quantification for RNA-seq
2.1.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.1.1Version of this port present on the latest quarterly branch.
Maintainer: mzaki@e-mail.ne.jp search for ports maintained by this maintainer
Port Added: 2018-07-11 21:32:56
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
License: MIT
Dependency lines:
  • stringtie>0:biology/stringtie
subread High-performance read alignment, quantification and mutation discovery
2.1.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.1.0Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2020-06-05 01:55:58
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
License: GPLv3
Dependency lines:
  • subread>0:biology/subread
tRNAscan-SE Searching for tRNA genes in genomic sequence
2.0.11 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.0.11Version of this port present on the latest quarterly branch.
Maintainer: mzaki@e-mail.ne.jp search for ports maintained by this maintainer
Port Added: 2002-03-27 14:19:04
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
License: GPLv3+
Dependency lines:
  • tRNAscan-SE>0:biology/tRNAscan-SE
tabixpp C++ wrapper to tabix indexer
1.1.2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.1.2Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-14 23:52:29
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
License: MIT
Dependency lines:
  • tabixpp>0:biology/tabixpp
taxonkit Practical and efficient NCBI taxonomy toolkit
0.19.0_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.19.0Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-05-26 22:27:16
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License: MIT
Dependency lines:
  • taxonkit>0:biology/taxonkit
treekin Efficient computation of RNA folding dynamics
0.5.1_7 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.5.1_7Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-06-15 20:37:22
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
License: LatticeLib
Dependency lines:
  • treekin>0:biology/treekin
treepuzzle Maximum likelihood phylogeny reconstruction using quartets
5.2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 5.2Version of this port present on the latest quarterly branch.
Maintainer: jan.lentfer@web.de search for ports maintained by this maintainer
Port Added: 2002-11-20 09:04:07
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License: not specified in port
Dependency lines:
  • treepuzzle>0:biology/treepuzzle
trimadap Trim adapter sequences from Illumina data using heuristic rules
0.1.4 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.1.4Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-03 18:24:21
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
License: MIT
Dependency lines:
  • trimadap>0:biology/trimadap
trimmomatic Flexible read trimming tool for Illumina NGS data
0.39 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.39Version of this port present on the latest quarterly branch.
There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2016-03-17 08:21:26
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Also Listed In: java
License: GPLv3
Dependency lines:
  • trimmomatic>0:biology/trimmomatic
ucsc-userapps Command line tools from the UCSC Genome Browser project
474 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 474Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-04-25 17:21:12
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: perl5 python
License: MIT
Dependency lines:
  • ucsc-userapps>0:biology/ucsc-userapps
ugene Integrated bioinformatics toolkit
40.1_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 40.1_1Version of this port present on the latest quarterly branch.
Maintainer: h2+fbsdports@fsfe.org search for ports maintained by this maintainer
Port Added: 2013-02-23 04:51:12
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Also Listed In: science
License: GPLv2+
Dependency lines:
  • ugene>0:biology/ugene
unikmer Toolkit for nucleic acid k-mer analysis, set operations on k-mers
0.20.0_6 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.20.0_4Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-05-26 22:27:12
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License: MIT
Dependency lines:
  • unikmer>0:biology/unikmer
vcf-split Split a multi-sample VCF into single-sample VCFs
0.1.5.10_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.1.5.10_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-03-21 15:17:34
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License: BSD2CLAUSE
Dependency lines:
  • vcf-split>0:biology/vcf-split
vcf2hap Generate .hap file from VCF for haplohseq
0.1.6.7_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.1.6.7_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-03-23 16:32:36
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License: BSD2CLAUSE
Dependency lines:
  • vcf2hap>0:biology/vcf2hap
vcflib C++ library and CLI tools for parsing and manipulating VCF files
1.0.13 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.0.12Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-17 03:11:48
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License: MIT
Dependency lines:
  • vcflib>0:biology/vcflib
vcftools Tools for working with VCF genomics files
0.1.17 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.1.16_2Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2016-02-26 17:08:07
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
License: LGPL3
Dependency lines:
  • vcftools>0:biology/vcftools
velvet Sequence assembler for very short reads
1.2.10_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.2.10_2Version of this port present on the latest quarterly branch.
Maintainer: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 2009-11-07 01:24:24
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
License: not specified in port
Dependency lines:
  • velvet>0:biology/velvet
viennarna Alignment tools for the structural analysis of RNA
2.7.0_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.7.0_1Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-06-24 09:29:23
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License: ViennaRNALicense
Dependency lines:
  • viennarna>0:biology/viennarna
vsearch Versatile open-source tool for metagenomics
2.30.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.30.0Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-05-09 21:29:03
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
License: GPLv3
Dependency lines:
  • vsearch>0:biology/vsearch
vt Discovers short variants from Next Generation Sequencing data
0.57721_3 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.57721_3Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2020-06-04 18:28:20
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
License: MIT
Dependency lines:
  • vt>0:biology/vt
wfa2-lib Exact gap-affine algorithm using homology to accelerate alignment
2.3.5 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.3.5Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2023-01-30 19:12:07
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
License: MIT
Dependency lines:
  • wfa2-lib>0:biology/wfa2-lib
wise Intelligent algorithms for DNA searches
2.4.1_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.4.1_1Version of this port present on the latest quarterly branch.
There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2002-09-10 13:59:05
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
License: BSD3CLAUSE GPLv2
Dependency lines:
  • wise>0:biology/wise
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