Category listing - biology |
Software related to biology.
- Number of ports in this category): 264
Ports marked with a * actually reside within another category but
have biology listed as a secondary category. |
- py-pymol OpenGL-based molecular visualization system
- 2.5.0.97_2* 2.5.0.97_2Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2017-12-19 19:49:25
- Also Listed In: python science
- License: PyMOL
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}pymol>0:science/py-pymol@${PY_FLAVOR}
- py-pyrodigal Python binding for Prodigal, an ORF finder for genomes and metagenomes
- 3.3.0 3.3.0Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2022-12-06 17:27:05
- Also Listed In: python
- License: GPLv3
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}pyrodigal>0:biology/py-pyrodigal@${PY_FLAVOR}
- py-pysam Python module for reading, manipulating and writing genomic data sets
- 0.22.0 0.22.0Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2017-05-06 06:30:42
- Also Listed In: python
- License: MIT
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR}
- py-python-libsbml LibSBML Python API
- 5.20.1 5.20.1Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2021-08-17 21:33:06
- Also Listed In: python
- License: LGPL21
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}python-libsbml>0:biology/py-python-libsbml@${PY_FLAVOR}
- py-pywgsim Modified wgsim genomic data simulator
- 0.5.2 0.5.2Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2021-09-06 12:57:08
- Also Listed In: python
- License: MIT
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}pywgsim>0:biology/py-pywgsim@${PY_FLAVOR}
- py-resdk Resolwe SDK to interact with Resolwe server and Resolwe Bioinformatics
- 21.1.0 20.0.0Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2021-04-20 04:24:12
- Also Listed In: python
- License: APACHE20
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}resdk>0:biology/py-resdk@${PY_FLAVOR}
- py-scikit-bio Data structures, algorithms, educational resources for bioinformatics
- 0.6.0 0.5.9Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2020-05-16 02:25:40
- Also Listed In: education python
- License: BSD3CLAUSE
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}scikit-bio>0:biology/py-scikit-bio@${PY_FLAVOR}
- py-valerius Python bioinformatics tools
- 0.2 0.2Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2022-10-04 04:09:26
- Also Listed In: python
- License: MIT
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}valerius>0:biology/py-valerius@${PY_FLAVOR}
- py-xenaPython API for Xena Hub to access genetic information shared through the hub
- 1.0.14 1.0.14Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2019-04-12 17:01:25
- Also Listed In: python
- License: APACHE20
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}xenaPython>0:biology/py-xenaPython@${PY_FLAVOR}
- pyfasta Fast, memory-efficient, pythonic access to fasta sequence files
- 0.5.2_5 0.5.2_5Version of this port present on the latest quarterly branch.
- Maintainer: wen@FreeBSD.org
- Port Added: 2009-11-18 05:53:48
- Also Listed In: python
- License: MIT
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}pyfasta>0:biology/pyfasta@${PY_FLAVOR}
- python-nexus Generic nexus file format reader for python
- 2.9.0 2.9.0Version of this port present on the latest quarterly branch.
- Maintainer: wen@FreeBSD.org
- Port Added: 2009-12-29 13:39:49
- Also Listed In: python
- License: BSD3CLAUSE
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}python-nexus>0:biology/python-nexus@${PY_FLAVOR}
- rainbow Efficient clustering and assembling of short reads, especially for RAD
- 2.0.4 2.0.4Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2018-04-02 16:50:56
- License: GPLv3+
- Dependency lines:
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- rainbow>0:biology/rainbow
- rampler Standalone module for sampling genomic sequences
- 2.0.0_1 2.0.0_1Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2021-01-19 09:50:02
- License: MIT
- Dependency lines:
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- rampler>0:biology/rampler
- raster3d Set of tools for generating raster images of proteins and molecules
- 3.0.7_3* 3.0.7_3Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2006-04-28 14:21:11
- People watching this port, also watch:: qca-qt5, geekcode, inn-current, psi
- Also Listed In: graphics
- License: ART20
- Dependency lines:
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- raster3d>0:graphics/raster3d
- readseq Read and reformat biosequences, Java command-line version
- 2.1.19 2.1.19Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2021-04-18 13:54:12
- Also Listed In: java
- License: PD
- Dependency lines:
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- readseq>0:biology/readseq
- rna-seq Metaport for RNA-Seq analysis
- 0.1.4 0.1.4Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2022-12-14 00:00:51
- Also Listed In: python
- License: NA
- Dependency lines:
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- rna-seq>0:biology/rna-seq
- ruby-bio Integrated environment for Bioinformatics written in Ruby
- 1.5.1 1.5.1Version of this port present on the latest quarterly branch.
- Maintainer: mauricio@arareko.net
- Port Added: 2001-10-24 03:21:52
- Also Listed In: ruby
- License: GPLv2 RUBY
- Dependency lines:
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- ruby30-bio>0:biology/ruby-bio
- rubygem-bio Integrated environment for Bioinformatics written in Ruby
- 2.0.5 2.0.5Version of this port present on the latest quarterly branch.
- Maintainer: ruby@FreeBSD.org
- Port Added: 2017-02-05 04:27:03
- Also Listed In: rubygems
- License: BSD2CLAUSE RUBY
- Dependency lines:
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- rubygem-bio>0:biology/rubygem-bio
- rubygem-bio-executables Collection of miscellaneous utilities for bioinformatics
- 1.0.0 1.0.0Version of this port present on the latest quarterly branch.
- Maintainer: sunpoet@FreeBSD.org
- Port Added: 2020-07-24 07:10:30
- Also Listed In: rubygems
- License: BSD2CLAUSE RUBY
- Dependency lines:
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- rubygem-bio-executables>0:biology/rubygem-bio-executables
- rubygem-bio-old-biofetch-emulator Emulate Bio::Fetch object
- 1.0.0 1.0.0Version of this port present on the latest quarterly branch.
- Maintainer: sunpoet@FreeBSD.org
- Port Added: 2020-07-24 07:10:45
- Also Listed In: rubygems
- License: MIT
- Dependency lines:
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- rubygem-bio-old-biofetch-emulator>0:biology/rubygem-bio-old-biofetch-emulator
- rubygem-bio-shell Command-line interface on BioRuby
- 1.0.1 1.0.1Version of this port present on the latest quarterly branch.
- Maintainer: sunpoet@FreeBSD.org
- Port Added: 2020-07-24 07:11:01
- Also Listed In: rubygems
- License: BSD2CLAUSE RUBY
- Dependency lines:
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- rubygem-bio-shell>0:biology/rubygem-bio-shell
- salmon Transcript-level quantification of RNA-seq from lightweight alignments
- 1.10.2_3 1.10.2_2Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2023-07-21 23:09:07
- License: GPLv3
- Dependency lines:
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- sam2pairwise Show pairwise alignment for each read in a SAM file
- 1.0.0 1.0.0Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2021-09-07 20:36:08
- License: MIT
- Dependency lines:
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- sam2pairwise>0:biology/sam2pairwise
- samtools Tools for manipulating next-generation sequencing data
- 1.17_1 1.17_1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2014-12-15 21:59:37
- License: MIT
- Dependency lines:
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- samtools>0:biology/samtools
- scrm Coalescent simulator for biological sequences
- 1.7.4_1 1.7.4_1Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2020-05-15 04:58:32
- License: GPLv3
- Dependency lines:
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- seaview Multiple DNA/protein sequence alignment editor
- 5.0.5_2,1 5.0.5_2,1Version of this port present on the latest quarterly branch.
- Maintainer: bofh@FreeBSD.org
- Port Added: unknown
- License: GPLv3
- Dependency lines:
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- seaview>0:biology/seaview
- seqan C++ sequence analysis template library
- 2.4.0 2.4.0Version of this port present on the latest quarterly branch.
- Maintainer: h2+fbsdports@fsfe.org
- Port Added: 2012-06-06 17:52:27
- License: BSD3CLAUSE
- Dependency lines:
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- seqan-apps Official bioinformatic applications based on the SeqAn library
- 2.4.0_11 2.4.0_11Version of this port present on the latest quarterly branch.
- Maintainer: h2+fbsdports@fsfe.org
- Port Added: 2016-05-10 00:52:12
- License: BSD3CLAUSE LGPL3 GPLv3
- Dependency lines:
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- seqan-apps>0:biology/seqan-apps
- seqan1 C++ Sequence Analysis Library
- 1.3.1_4 1.3.1_4Version of this port present on the latest quarterly branch.
- Maintainer: h2+fbsdports@fsfe.org
- Port Added: 2016-05-10 01:05:34
- License: BSD3CLAUSE
- Dependency lines:
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- seqan3 C++ header-only library for biological sequence analysis
- 3.3.0 3.3.0Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2021-05-12 01:24:05
- Also Listed In: devel math
- License: BSD3CLAUSE
- Dependency lines:
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- seqkit Cross-platform and ultrafast toolkit for FASTA/Q file manipulation
- 2.8.1_1 2.8.0_1Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2021-04-16 21:06:12
- License: MIT
- Dependency lines:
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- seqtk Tool for processing sequences in FASTA/FASTQ format
- 1.4 1.4Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2018-04-03 20:57:19
- License: GPLv2
- Dependency lines:
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- seqwish Alignment to variation graph inducer
- 0.7.9 0.7.9Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2023-07-21 21:42:05
- License: MIT
- Dependency lines:
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- seqwish>0:biology/seqwish
- sigviewer Viewing application for biosignals
- 0.6.4.13_2 0.6.4.13_2Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2021-08-17 07:06:07
- License: GPLv3
- Dependency lines:
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- sigviewer>0:biology/sigviewer
- simbody Multibody dynamics library for (bio)mechanical systems simulation
- 3.7_6* 3.7_6Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2018-11-15 06:47:08
- Also Listed In: science
- License: APACHE20
- Dependency lines:
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- simbody>0:science/simbody
- slclust Single-linkage clustering with Jaccard similarity
- 2010.02.02 2010.02.02Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2016-03-23 11:00:52
- License: ART10
- Dependency lines:
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- slclust>0:biology/slclust
- smithwaterman Smith-waterman-gotoh alignment algorithm
- g20160702 g20160702Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2018-04-15 17:46:20
- License: GPLv2
- Dependency lines:
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- smithwaterman>0:biology/smithwaterman
- snpeff Genetic variant annotation and effect prediction toolbox
- 5.1 5.1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2021-04-18 18:48:08
- Also Listed In: java python
- License: MIT
- Dependency lines:
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- spoa C++ implementation of the partial order alignment (POA) algorithm
- 4.1.0 4.1.0Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2021-01-19 09:28:06
- License: MIT
- Dependency lines:
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- sra-tools NCBI's toolkit for handling data in INSDC Sequence Read Archives
- 3.0.6 3.0.6Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2021-06-22 18:00:14
- Also Listed In: java
- License: PD LGPL21+
- Dependency lines:
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- sra-tools>0:biology/sra-tools
- stacks Software pipeline for building loci from short-read sequences
- 2.4_2 2.4_2Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2018-03-31 13:16:34
- Also Listed In: perl5 python
- License: GPLv2
- Dependency lines:
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- star Spliced Transcripts Alignment to a Reference
- 2.7.11.a_1 2.7.11.a_1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2019-04-21 20:31:13
- License: GPLv3
- Dependency lines:
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- stringtie Transcript assembly and quantification for RNA-seq
- 2.1.1 2.1.1Version of this port present on the latest quarterly branch.
- Maintainer: mzaki@e-mail.ne.jp
- Port Added: 2018-07-11 21:32:56
- License: MIT
- Dependency lines:
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- stringtie>0:biology/stringtie
- subread High-performance read alignment, quantification and mutation discovery
- 2.0.2 2.0.2Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2020-06-05 01:55:58
- License: GPLv3
- Dependency lines:
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- subread>0:biology/subread
- tRNAscan-SE Searching for tRNA genes in genomic sequence
- 2.0.11 2.0.11Version of this port present on the latest quarterly branch.
- Maintainer: mzaki@e-mail.ne.jp
- Port Added: 2002-03-27 14:19:04
- License: GPLv3+
- Dependency lines:
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- tRNAscan-SE>0:biology/tRNAscan-SE
- tabixpp C++ wrapper to tabix indexer
- 1.0.0.10_2 1.0.0.10_2Version of this port present on the latest quarterly branch.
- DEPRECATED: Dependent ports use git submodules now
- Maintainer: jwb@FreeBSD.org
- Port Added: 2018-04-14 23:52:29
- License: MIT
- Dependency lines:
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- tabixpp>0:biology/tabixpp
- taxonkit Practical and efficient NCBI taxonomy toolkit
- 0.16.0_2 0.16.0_2Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2021-05-26 22:27:16
- License: MIT
- Dependency lines:
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- taxonkit>0:biology/taxonkit
- treekin Efficient computation of RNA folding dynamics
- 0.5.1_6 0.5.1_6Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2019-06-15 20:37:22
- License: LatticeLib
- Dependency lines:
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- treekin>0:biology/treekin
- treepuzzle Maximum likelihood phylogeny reconstruction using quartets
- 5.2 5.2Version of this port present on the latest quarterly branch.
- Maintainer: jan.lentfer@web.de
- Port Added: 2002-11-20 09:04:07
- License: not specified in port
- Dependency lines:
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- treepuzzle>0:biology/treepuzzle
- trimadap Trim adapter sequences from Illumina data using heuristic rules
- 0.1.3_1 0.1.3_1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2018-04-03 18:24:21
- License: GPLv2
- Dependency lines:
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- trimadap>0:biology/trimadap
- trimmomatic Flexible read trimming tool for Illumina NGS data
- 0.39 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
- Port Added: 2016-03-17 08:21:26
- Also Listed In: java
- License: GPLv3
- Dependency lines:
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- trimmomatic>0:biology/trimmomatic
- ucsc-userapps Command line tools from the UCSC Genome Browser project
- 414_1 414_1Version of this port present on the latest quarterly branch.
- RESTRICTED: Redistribution is limited, see license
- Maintainer: jwb@FreeBSD.org
- Port Added: 2021-04-25 17:21:12
- Also Listed In: perl5 python
- License: UCSC-GB
- Dependency lines:
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- ucsc-userapps>0:biology/ucsc-userapps
- ugene Integrated bioinformatics toolkit
- 40.1_1 40.1_1Version of this port present on the latest quarterly branch.
- Maintainer: h2+fbsdports@fsfe.org
- Port Added: 2013-02-23 04:51:12
- Also Listed In: science
- License: GPLv2+
- Dependency lines:
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- unikmer Toolkit for nucleic acid k-mer analysis, set operations on k-mers
- 0.19.1_12 0.19.1_12Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2021-05-26 22:27:12
- License: MIT
- Dependency lines:
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- unikmer>0:biology/unikmer
- vcf-split Split a multi-sample VCF into single-sample VCFs
- 0.1.5.10_1 0.1.5.10_1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2021-03-21 15:17:34
- License: BSD2CLAUSE
- Dependency lines:
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- vcf-split>0:biology/vcf-split
- vcf2hap Generate .hap file from VCF for haplohseq
- 0.1.6.7_1 0.1.6.7_1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2021-03-23 16:32:36
- License: BSD2CLAUSE
- Dependency lines:
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- vcf2hap>0:biology/vcf2hap
- vcflib C++ library and CLI tools for parsing and manipulating VCF files
- 1.0.7_1 1.0.7_1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2018-04-17 03:11:48
- License: MIT
- Dependency lines:
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- vcftools Tools for working with VCF genomics files
- 0.1.16_2 0.1.16_2Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2016-02-26 17:08:07
- License: LGPL3
- Dependency lines:
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- vcftools>0:biology/vcftools
- velvet Sequence assembler for very short reads
- 1.2.10_2 1.2.10_2Version of this port present on the latest quarterly branch.
- Maintainer: mzaki@m.u-tokyo.ac.jp
- Port Added: 2009-11-07 01:24:24
- License: not specified in port
- Dependency lines:
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- viennarna Alignment tools for the structural analysis of RNA
- 2.6.4_2 2.6.4_2Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2019-06-24 09:29:23
- License: ViennaRNALicense
- Dependency lines:
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- viennarna>0:biology/viennarna
- vsearch Versatile open-source tool for metagenomics
- 2.27.1 2.27.0_1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2019-05-09 21:29:03
- License: GPLv3
- Dependency lines:
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- vsearch>0:biology/vsearch
- vt Discovers short variants from Next Generation Sequencing data
- 0.57721_3 0.57721_3Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2020-06-04 18:28:20
- License: MIT
- Dependency lines:
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- wfa2-lib Exact gap-affine algorithm using homology to accelerate alignment
- 2.3.4 2.3.4Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2023-01-30 19:12:07
- License: MIT
- Dependency lines:
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- wfa2-lib>0:biology/wfa2-lib
- wise Intelligent algorithms for DNA searches
- 2.4.1_1 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
- Port Added: 2002-09-10 13:59:05
- License: BSD3CLAUSE GPLv2
- Dependency lines:
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