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

libgff GFF/GTF parsing library based on GCLib

2.0.0 2.0.0Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2021-12-05 20:51:11

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License: BSL

Dependency lines:

• libgff>0:biology/libgff

libgtextutils Gordon's text utilities

0.7 0.7Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2015-09-25 18:31:38

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: AGPLv3

Dependency lines:

• libgtextutils>0:biology/libgtextutils

libneurosim Common interfaces for neuronal simulators

1.2.0_1 1.2.0_1Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2021-10-08 17:21:18

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: GPLv3

Dependency lines:

• libneurosim>0:biology/libneurosim

libnuml C++ library for Numerical Markup Language

1.1.6 1.1.6Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2021-09-19 06:51:03

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: devel

License: LGPL21

Dependency lines:

• libnuml>0:biology/libnuml

libsbml API Library for Working with SBML File

5.20.4_1 5.20.4_1Version of this port present on the latest quarterly branch.

Maintainer: sunpoet@FreeBSD.org

Port Added: 2009-05-28 23:36:42

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: devel

License: LGPL21

Dependency lines:

• libsbml>0:biology/libsbml

libsedml C++ SED-ML library

2.0.32 2.0.32Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2021-09-19 18:18:23

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: devel

License: BSD2CLAUSE

Dependency lines:

• libsedml>0:biology/libsedml

linux-foldingathome Folding@home Client

8.4.9 7.6.21Version of this port present on the latest quarterly branch.

Maintainer: 0mp@FreeBSD.org

Port Added: 2006-08-28 22:34:01

People watching this port, also watch:: OpenSP, mDNSResponder, p5-MIME-Tools, vcdimager, libexif

Also Listed In: linux

License: FAHSL

Dependency lines:

• linux-foldingathome>0:biology/linux-foldingathome

locarna LocARNA provides several tools for the structural analysis of RNA

2.0.0_1 2.0.0_1Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2023-07-16 21:57:10

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: GPLv3

Dependency lines:

• locarna>0:biology/locarna

mafft Multiple alignment program for amino acid or nucleotide sequences

7.267_1 7.267_1Version of this port present on the latest quarterly branch.

Maintainer: cartwright@asu.edu

Port Added: 2006-03-15 10:41:45

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: BSD2CLAUSE

Dependency lines:

• mafft>0:biology/mafft

mapm3 Constructs linkage maps of markers segregating in experimental crosses

3.0_1 3.0_1Version of this port present on the latest quarterly branch.

Maintainer: tphilipp@potion-studios.com

Port Added: 2008-04-06 04:49:23

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: MAPMAKER

Dependency lines:

• mapm3>0:biology/mapm3

mashmap Fast approximate aligner for long DNA sequences

3.1.3 3.1.3Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2023-07-11 01:45:07

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: PD

Dependency lines:

• mashmap>0:biology/mashmap

mca-calling Core tools for Mosaic Chromosomal Alteration event calling

0.1.0 0.1.0Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2024-10-24 13:33:04

License: NA

Dependency lines:

• mca-calling>0:biology/mca-calling

megahit Ultra-fast single-node large and complex metagenomics assembly

1.2.9_1 1.2.9_1Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2022-11-22 16:42:09

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: GPLv3

Dependency lines:

• megahit>0:biology/megahit

metaeuk Gene discovery and annotation for large-scale eukaryotic metagenomics

7 7Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2022-11-26 11:18:05

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: GPLv3

Dependency lines:

• metaeuk>0:biology/metaeuk

migrate Program to estimate population sizes and migration rates

5.0.6_2 5.0.6_2Version of this port present on the latest quarterly branch.

Maintainer: eduardo@FreeBSD.org

Port Added: 2001-08-06 10:07:46

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: MIT

Dependency lines:

• migrate>0:biology/migrate

minc2 Medical Imaging NetCDF

2.2.00_15,1^* 2.2.00_15,1Version 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: 2006-04-30 12:09:06

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: science

License: MIT

Dependency lines:

• minc2>0:science/minc2

minimap2 Pairwise aligner for genomic and spliced nucleotide sequences

2.28_1 2.28_1Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2019-04-24 18:04:07

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: MIT

Dependency lines:

• minimap2>0:biology/minimap2

mmseqs2 Ultra fast and sensitive sequence search and clustering suite

17.b804.f 13.45111_2Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2021-06-24 17:33:13

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: GPLv3

Dependency lines:

• MMseqs2>0:biology/mmseqs2

mmtf-cpp C++ MMTF format API, decoder and encoder, for molecular structures

1.1.0_1^* 1.1.0_1Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2019-02-16 10:48:32

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Also Listed In: science

License: MIT

Dependency lines:

• mmtf-cpp>0:science/mmtf-cpp

molden Display molecular orbitals and electron densities in 2D and 3D

7.1_1,1 7.1_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: unknown

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: Molden

Dependency lines:

• molden>0:biology/molden

mothur Software for bioinformatics of the microbial ecology community

1.48.2 1.48.2Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2019-05-20 17:59:35

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: GPLv3

Dependency lines:

• mothur>0:biology/mothur

mrbayes Bayesian inference of phylogeny

3.2.7_2 3.2.7_2Version of this port present on the latest quarterly branch.

Maintainer: mzaki@e-mail.ne.jp

Port Added: 2007-12-15 15:13:49

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: GPLv3

Dependency lines:

• mrbayes>0:biology/mrbayes

mummer Modular system for rapid whole genome alignment

4.0.1 4.0.0.r1.20240427Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2007-12-14 20:56:11

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: ART10

Dependency lines:

• mummer>0:biology/mummer

muscle MUltiple Sequence Comparison by Log-Expectation

3.8.1551 3.8.1551Version of this port present on the latest quarterly branch.

Maintainer: mzaki@e-mail.ne.jp

Port Added: 2008-05-14 13:52:50

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: PD

Dependency lines:

• muscle>0:biology/muscle

ncbi-blast+ NCBI implementation of Basic Local Alignment Search Tool

2.16.0_3 2.14.1_8Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2014-12-30 20:03:26

People watching this port, also watch:: xrdp, telegram-desktop, osv-scanner, memcached, R

Also Listed In: perl5 python

License: PD

Dependency lines:

• ncbi-blast+>0:biology/ncbi-blast+

ncbi-cxx-toolkit NCBI C++ Toolkit

29.0.1 28.0.11Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2018-10-08 07:55:03

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: devel science

License: PD

Dependency lines:

• ncbi-cxx-toolkit>0:biology/ncbi-cxx-toolkit

ncbi-entrez-direct Access to the NCBI's suite of interconnected databases

14.9.20210423_25 14.9.20210423_24Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2021-04-24 23:42:15

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: perl5

License: PD

Dependency lines:

• ncbi-entrez-direct>0:biology/ncbi-entrez-direct

ncbi-toolkit NCBI development toolkit, including BLAST 2 and GenBank/Entrez support

2017.01.06_9 2017.01.06_9Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2000-10-29 10:56:24

People watching this port, also watch:: libglade2, xorg-fonts-truetype, libexif, R, p5-libwww

License: not specified in port

Dependency lines:

• ncbi-toolkit>0:biology/ncbi-toolkit

nest Simulator for spiking neural network models

3.8_3^* 3.8_2Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2019-05-11 20:30:18

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: science

License: GPLv2

Dependency lines:

• nest>0:science/nest

ngs-sdk Tools and libraries for using data in the INSDC Sequence Read Archives

3.0.1 3.0.1Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2018-06-10 23:58:19

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: PD

Dependency lines:

• ngs-sdk>0:biology/ngs-sdk

p5-AcePerl Perl5 interface to the ACEDB genome database system

1.92_5 1.92_5Version of this port present on the latest quarterly branch.

Maintainer: perl@FreeBSD.org

Port Added: 2000-07-28 10:16:10

People watching this port, also watch:: p5-Crypt-DSA, p5-IPC-Shareable, pure-ftpd, p5-Event, libglade2

Also Listed In: databases perl5

License: ART10 GPLv1+

Dependency lines:

• p5-AcePerl>0:biology/p5-AcePerl

p5-Bio-ASN1-EntrezGene Regular expression-based Perl Parser for NCBI Entrez Gene

1.73_2,1 1.73_2,1Version of this port present on the latest quarterly branch.

Maintainer: sunpoet@FreeBSD.org

Port Added: 2005-10-15 20:11:03

People watching this port, also watch:: p5-Syntax-Highlight-Perl-Improved, p5-XML-DOM-XPath, py311-biopython, py311-Automat, py311-PyOpenGL

Also Listed In: perl5

License: ART10 GPLv1+

Dependency lines:

• p5-Bio-ASN1-EntrezGene>0:biology/p5-Bio-ASN1-EntrezGene

p5-Bio-Cluster BioPerl cluster modules

1.7.3_1 1.7.3_1Version of this port present on the latest quarterly branch.

Maintainer: sunpoet@FreeBSD.org

Port Added: 2019-02-20 20:47:05

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: perl5

License: ART10 GPLv1+

Dependency lines:

• p5-Bio-Cluster>0:biology/p5-Bio-Cluster

p5-Bio-Coordinate Modules for working with biological coordinates

1.007001 1.007001Version of this port present on the latest quarterly branch.

Maintainer: sunpoet@FreeBSD.org

Port Added: 2016-12-19 16:00:37

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: perl5

License: ART10 GPLv1+

Dependency lines:

• p5-Bio-Coordinate>0:biology/p5-Bio-Coordinate

p5-Bio-DB-EMBL Database object interface for EMBL entry retrieval

1.7.4 1.7.4Version of this port present on the latest quarterly branch.

Maintainer: sunpoet@FreeBSD.org

Port Added: 2019-12-08 16:52:22

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: perl5

License: ART10 GPLv1+

Dependency lines:

• p5-Bio-DB-EMBL>0:biology/p5-Bio-DB-EMBL

p5-Bio-DB-NCBIHelper Collection of routines useful for queries to NCBI databases

1.7.8 1.7.8Version of this port present on the latest quarterly branch.

Maintainer: sunpoet@FreeBSD.org

Port Added: 2019-12-08 16:52:43

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: perl5

License: ART10 GPLv1+

Dependency lines:

• p5-Bio-DB-NCBIHelper>0:biology/p5-Bio-DB-NCBIHelper

p5-Bio-Das Client-side library for Distributed Genome Annotation System

1.17_4 1.17_4Version of this port present on the latest quarterly branch.

Maintainer: perl@FreeBSD.org

Port Added: 2005-09-01 13:10:39

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: perl5

License: ART10 GPLv1+

Dependency lines:

• p5-Bio-Das>0:biology/p5-Bio-Das

p5-Bio-Das-Lite Perl extension for the DAS (HTTP+XML) Protocol

2.11_1 2.11_1Version of this port present on the latest quarterly branch.

Maintainer: perl@FreeBSD.org

Port Added: 2010-03-01 09:16:56

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: perl5

License: ART10 GPLv1+

Dependency lines:

• p5-Bio-Das-Lite>0:biology/p5-Bio-Das-Lite

p5-Bio-FeatureIO Handler for FeatureIO

1.6.905 1.6.905Version of this port present on the latest quarterly branch.

Maintainer: sunpoet@FreeBSD.org

Port Added: 2017-09-15 19:17:29

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: perl5

License: ART10 GPLv1+

Dependency lines:

• p5-Bio-FeatureIO>0:biology/p5-Bio-FeatureIO

p5-Bio-GFF3 Fast low-level functions for parsing and formatting GFF3

2.0_2 2.0_2Version of this port present on the latest quarterly branch.

Maintainer: perl@FreeBSD.org

Port Added: 2011-04-22 08:51:49

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: perl5

License: ART10 GPLv1+

Dependency lines:

• p5-Bio-GFF3>0:biology/p5-Bio-GFF3

p5-Bio-Glite Perl Interface to G-language

0.10_2 0.10_2Version of this port present on the latest quarterly branch.

Maintainer: perl@FreeBSD.org

Port Added: 2009-04-02 18:25:38

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: perl5

License: not specified in port

Dependency lines:

• p5-Bio-Glite>0:biology/p5-Bio-Glite

p5-Bio-Graphics Generate GD Images of Bio::Seq Objects

2.40_2 2.40_2Version of this port present on the latest quarterly branch.

Maintainer: perl@FreeBSD.org

Port Added: 2009-03-10 18:52:27

People watching this port, also watch:: zh-opencc, snd, p5-HTML-HTML5-Entities, xorg-docs, p5-Ubic

Also Listed In: perl5

License: ART10 GPLv1+

Dependency lines:

• p5-Bio-Graphics>0:biology/p5-Bio-Graphics

p5-Bio-MAGETAB Data model and utility API for the MAGE-TAB format

1.31_2 1.31_2Version of this port present on the latest quarterly branch.

Maintainer: perl@FreeBSD.org

Port Added: 2009-07-01 09:03:56

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: perl5

License: GPLv2

Dependency lines:

• p5-Bio-MAGETAB>0:biology/p5-Bio-MAGETAB

p5-Bio-NEXUS Object-oriented Perl API for the NEXUS file format

0.78_1 0.78_1Version of this port present on the latest quarterly branch.

Maintainer: perl@FreeBSD.org

Port Added: 2009-08-22 20:40:26

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: perl5

License: not specified in port

Dependency lines:

• p5-Bio-NEXUS>0:biology/p5-Bio-NEXUS

p5-Bio-Phylo Phylogenetic analysis using Perl

2.0.1 2.0.1Version of this port present on the latest quarterly branch.

Maintainer: perl@FreeBSD.org

Port Added: 2006-05-13 16:50:16

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Also Listed In: perl5

License: ART10 GPLv1+

Dependency lines:

• p5-Bio-Phylo>0:biology/p5-Bio-Phylo

p5-Bio-SCF Read and Update SCF Chromatographic Sequence Files

1.03_2 1.03_2Version of this port present on the latest quarterly branch.

Maintainer: wen@FreeBSD.org

Port Added: 2009-08-28 23:38:55

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: perl5

License: ART10 GPLv1+

Dependency lines:

• p5-Bio-SCF>0:biology/p5-Bio-SCF

p5-Bio-Variation BioPerl variation-related functionality

1.7.5 1.7.5Version of this port present on the latest quarterly branch.

Maintainer: sunpoet@FreeBSD.org

Port Added: 2019-12-08 16:53:05

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: perl5

License: ART10 GPLv1+

Dependency lines:

• p5-Bio-Variation>0:biology/p5-Bio-Variation

p5-BioPerl Collection of Perl modules for bioinformatics

1.007008 1.007008Version of this port present on the latest quarterly branch.

Maintainer: sunpoet@FreeBSD.org

Port Added: 2016-12-18 15:27:08

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: perl5

License: ART10 GPLv1+

Dependency lines:

• p5-BioPerl>0:biology/p5-BioPerl

p5-BioPerl-Run Wrapper modules for common bioinformatics tools

1.007003 1.007003Version of this port present on the latest quarterly branch.

Maintainer: sunpoet@FreeBSD.org

Port Added: 2016-12-18 15:29:01

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: perl5

License: ART10 GPLv1+

Dependency lines:

• p5-BioPerl-Run>0:biology/p5-BioPerl-Run

p5-TrimGalore Wrapper around Cutadapt and FastQC for adapter and quality trimming

0.6.10 0.6.10Version 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: 2017-12-09 13:23:40

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: perl5 python

License: GPLv3

Dependency lines:

• p5-TrimGalore>0:biology/p5-TrimGalore

p5-transdecoder Identify candidate coding regions within transcript sequences

5.7.1 5.7.1Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2016-03-16 20:12:42

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Also Listed In: perl5

License: BSD3CLAUSE

Dependency lines:

• p5-transdecoder>0:biology/p5-transdecoder

paml Phylogenetic Analysis by Maximum Likelihood (PAML)

4.10.7 4.10.7Version of this port present on the latest quarterly branch.

Maintainer: jrm@FreeBSD.org

Port Added: 2000-07-10 00:21:06

People watching this port, also watch:: xorg-docs, libexif, libXdamage, libevent, xdm

License: GPLv3

Dependency lines:

• paml>0:biology/paml

pbbam PacBio BAM C++ library, with SWIG bindings

0.18.0_11 0.18.0_10Version 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: 2018-04-23 16:08:32

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License: BSD3CLAUSE

Dependency lines:

• pbbam>0:biology/pbbam

peak-classifier Classify ChIP/ATAC-Seq peaks based on features provided in a GFF

0.1.4.13_1 0.1.4.13_1Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2021-06-14 16:45:08

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: BSD2CLAUSE

Dependency lines:

• peak-classifier>0:biology/peak-classifier

pear-merger Memory-efficient and highly accurate paired-end read merger

0.9.6_1 0.9.6_1Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2018-04-04 17:21:55

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: CC-BY-NC-SA-3.0

Dependency lines:

• pear-merger>0:biology/pear-merger

phrap Program for assembling shotgun DNA sequence data

1.090518 1.090518Version of this port present on the latest quarterly branch.

IGNORE: you must request the source code \(distrib.tar.gz\) via e-mail, place it manually in /usr/ports/distfiles/phrap, and then try it again

Maintainer: mzaki@m.u-tokyo.ac.jp

Port Added: 2008-05-24 07:03:43

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License: PHRAP

Dependency lines:

• phrap>0:biology/phrap

phred Base calling and quality value assignment on DNA sequencing

0.020425.c 0.020425.cVersion of this port present on the latest quarterly branch.

Maintainer: mzaki@m.u-tokyo.ac.jp

Port Added: 2008-05-24 07:05:09

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License: PHRED

Dependency lines:

• phred>0:biology/phred

phyml Simple, fast, and accurate algorithm to estimate large phylogenies

3.3.20220408_1,1 3.3.20220408_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: 2009-07-21 01:10:33

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License: GPLv3

Dependency lines:

• phyml>0:biology/phyml

picard-tools CLI tools for manipulating high-throughput sequencing (HTS) data

2.22.9 2.22.9Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2020-06-13 13:54:53

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Also Listed In: java

License: MIT

Dependency lines:

• picard-tools>0:biology/picard-tools

plink Whole genome association analysis toolset

1.90.b6.17_5 1.90.b6.17_4Version of this port present on the latest quarterly branch.

Maintainer: mzaki@e-mail.ne.jp

Port Added: 2012-09-27 10:00:09

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License: GPLv3

Dependency lines:

• plink>0:biology/plink

pooler Optimise DNA sequencing primer-set combinations

1.89 1.88_1Version of this port present on the latest quarterly branch.

Maintainer: ssb22@cam.ac.uk

Port Added: 2020-11-15 19:32:44

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License: APACHE20

Dependency lines:

• pooler>0:biology/pooler

preseq Predict yield of distinct reads from a genomic library

3.2.0 3.2.0Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2024-11-22 20:39:08

License: GPLv3

Dependency lines:

• preseq>0:biology/preseq

primer3 Primer3 helps to choose primers for PCR reactions

2.3.6 2.3.6Version 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: 2002-09-17 15:31:31

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License: GPLv2

Dependency lines:

• primer3>0:biology/primer3

prodigal Protein-coding gene prediction for prokaryotic genomes

2.6.3.16 2.6.3.16Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2019-02-03 18:08:28

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License: GPLv3

Dependency lines:

• prodigal>0:biology/prodigal

prodigy-lig Prediction of protein-small molecule binding affinities

1.1.3 1.1.3Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2019-02-03 18:49:38

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Also Listed In: python

License: APACHE20

Dependency lines:

• prodigy-lig>0:biology/prodigy-lig

protomol OO, component based, framework for molecular dynamics (MD) simulations

2.0.3_16 2.0.3_16Version 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: 2006-05-05 20:12:57

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License: GPLv2

Dependency lines:

• protomol>0:biology/protomol

psi88 Plotting wavefunctions (molecular orbitals) in 3D

1.0_17 1.0_17Version 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: unknown

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

License: not specified in port

Dependency lines:

• psi88>0:biology/psi88

py-Genesis-PyAPI API for the Genesis platform for genetics information processing

1.2.1_1 1.2.1Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2018-06-13 01:46:31

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Also Listed In: python

License: APACHE20

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}Genesis-PyAPI>0:biology/py-Genesis-PyAPI@${PY_FLAVOR}

py-PySCeS Python Simulator for Cellular Systems

1.2.2 1.2.2Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2021-08-17 21:33:11

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Also Listed In: python

License: BSD3CLAUSE

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}pysces>0:biology/py-PySCeS@${PY_FLAVOR}

py-atomium Molecular modeller and file parser

1.0.11_3^* 1.0.11_2Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2022-10-04 04:09:29

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Also Listed In: python science

License: MIT

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}atomium>0:science/py-atomium@${PY_FLAVOR}

py-bcbio-gff Read and write Generic Feature Format (GFF) with Biopython integration

0.7.1_1 0.7.0Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2022-02-03 19:39:09

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Also Listed In: python

License: BSD3CLAUSE

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}bcbio-gff>0:biology/py-bcbio-gff@${PY_FLAVOR}

py-biom-format Biological Observation Matrix (BIOM) Format Project

2.1.16_1 2.1.16Version of this port present on the latest quarterly branch.

Maintainer: jrm@FreeBSD.org

Port Added: 2016-05-09 16:37:53

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Also Listed In: python

License: BSD3CLAUSE

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}biom-format>0:biology/py-biom-format@${PY_FLAVOR}

py-biopython Collection of Python modules for bioinformatics

1.85_1 1.83Version of this port present on the latest quarterly branch.

Maintainer: mauricio@arareko.net

Port Added: 2000-07-31 09:12:24

People watching this port, also watch:: python, chkrootkit, py311-psycopg, autoconf, cops

Also Listed In: python

License: BSD3CLAUSE

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}biopython>0:biology/py-biopython@${PY_FLAVOR}

py-biosig Library for reading and writing different biosignal data format

2.6.1_1 2.6.1Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2022-12-30 08:33:19

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License: GPLv3

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}biosig>0:biology/py-biosig@${PY_FLAVOR}

py-bx-python Python module for reading, manipulating and writing genomic data sets

0.13.0_1 0.13.0Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2017-05-06 06:28:34

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Also Listed In: python

License: MIT

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}bx-python>0:biology/py-bx-python@${PY_FLAVOR}

py-chainer-chemistry Library for deep learning in biology and chemistry

0.7.1_2^* 0.7.1_1Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2019-08-08 21:06:54

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Also Listed In: science

License: MIT

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}chainer-chemistry>0:science/py-chainer-chemistry@${PY_FLAVOR}

py-crossmap Lift over genomics coordinates between assemblies

0.7.3_1 0.5.4_1Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2021-04-12 23:39:05

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Also Listed In: python

License: GPLv3+

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}crossmap>0:biology/py-crossmap@${PY_FLAVOR}

py-cutadapt Trim adapters from high-throughput sequencing reads

5.0_1 4.9Version of this port present on the latest quarterly branch.

Maintainer: jadawin@FreeBSD.org

Port Added: 2017-11-29 22:17:53

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Also Listed In: python

License: MIT

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}cutadapt>0:biology/py-cutadapt@${PY_FLAVOR}

py-deap Distributed Evolutionary Algorithms in Python

1.4.1_1^* 1.4.1Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2018-12-07 07:46:27

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: devel math python science

License: GPLv3

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}deap>0:math/py-deap@${PY_FLAVOR}

py-deeptools User-friendly tools for exploring deep-sequencing data

3.5.2_1 3.5.2Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2021-10-14 11:57:05

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Also Listed In: python

License: BSD3CLAUSE

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}deepTools>0:biology/py-deeptools@${PY_FLAVOR}

py-deeptoolsintervals Python interface for deepTools interval trees

0.1.9_1 0.1.9Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2021-10-13 16:06:15

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Also Listed In: python

License: MIT

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}deeptoolsintervals>0:biology/py-deeptoolsintervals@${PY_FLAVOR}

py-dna-features-viewer Python library to visualize DNA features, e.g. GenBank or Gff files

3.1.3_1 3.1.3Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2022-02-03 12:42:05

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Also Listed In: python

License: MIT

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}dna-features-viewer>0:biology/py-dna-features-viewer@${PY_FLAVOR}

py-dnaio Read and write FASTQ and FASTA

1.2.3 1.2.3Version of this port present on the latest quarterly branch.

Maintainer: wen@FreeBSD.org

Port Added: 2019-03-24 19:40:53

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Also Listed In: python

License: MIT

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}dnaio>0:biology/py-dnaio@${PY_FLAVOR}

py-ete3 Framework for the analysis and visualization of trees

3.1.3_1 3.1.3Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2020-05-16 00:13:16

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Also Listed In: python

License: GPLv3

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}ete3>0:biology/py-ete3@${PY_FLAVOR}

py-gffutils Work with GFF and GTF files in a flexible database framework

0.13_1 0.13Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2018-10-19 02:07:07

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Also Listed In: python

License: MIT

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}gffutils>0:biology/py-gffutils@${PY_FLAVOR}

py-goatools Tools for processing and visualizing Gene Ontology terms

1.1.6_2 1.1.6_1Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2021-07-02 17:03:13

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Also Listed In: python

License: BSD2CLAUSE

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}goatools>0:biology/py-goatools@${PY_FLAVOR}

py-gtfparse Parsing tools for GTF (gene transfer format) files

2.5.0 2.5.0Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2018-10-19 02:03:55

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Also Listed In: python

License: APACHE20

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}gtfparse>0:biology/py-gtfparse@${PY_FLAVOR}

py-hits Utilities for processing high-throughput sequencing experiments

0.1_1 0.1Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2020-05-16 03:11:12

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Also Listed In: python

License: GPLv3

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}hits>0:biology/py-hits@${PY_FLAVOR}

py-htseq Python library to facilitate programmatic analysis of sequence data

2.0.9_1 2.0.9Version of this port present on the latest quarterly branch.

Maintainer: alster@vinterdalen.se

Port Added: 2023-07-28 15:45:06

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Also Listed In: python

License: GPLv3

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}HTSeq>0:biology/py-htseq@${PY_FLAVOR}

py-libnuml Numerical Markup Language for Python

1.1.6 1.1.6Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2021-09-19 06:51:08

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Also Listed In: devel

License: LGPL21

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}libnuml>0:biology/py-libnuml@${PY_FLAVOR}

py-libsedml SED-ML library for Python

2.0.32 2.0.32Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2021-09-19 18:18:25

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Also Listed In: devel

License: BSD2CLAUSE

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}libsedml>0:biology/py-libsedml@${PY_FLAVOR}

py-loompy Work with .loom files for single-cell RNA-seq data

3.0.7_2 3.0.7_1Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2018-09-21 08:05:03

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: python

License: BSD2CLAUSE

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}loompy>0:biology/py-loompy@${PY_FLAVOR}

py-macs2 Identify transcription factor binding sites

2.2.9.1_1 2.2.9.1Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2017-12-02 20:46:35

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Also Listed In: python

License: BSD3CLAUSE

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}macs2>0:biology/py-macs2@${PY_FLAVOR}

py-macs3 Peak caller aimed at transcription factor binding sites

3.0.3 3.0.2Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2024-01-10 15:21:08

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Also Listed In: python

License: BSD3CLAUSE

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}MACS3>0:biology/py-macs3@${PY_FLAVOR}

py-mmcif mmCIF Core Access Library

0.90.0_1^* 0.90.0Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2022-10-04 01:36:47

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Also Listed In: python science

License: APACHE20

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}mmcif>0:science/py-mmcif@${PY_FLAVOR}

py-mrcfile MRC file I/O library which is used in structural biology

1.5.3_1 1.5.3Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2022-05-01 17:39:29

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Also Listed In: python

License: BSD3CLAUSE

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}mrcfile>0:biology/py-mrcfile@${PY_FLAVOR}

py-multiqc Aggregate bioinformatics analysis reports across samples and tools

1.25.2_2 1.25.2_1Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2019-09-23 16:09:36

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Also Listed In: python

License: GPLv3

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}multiqc>0:biology/py-multiqc@${PY_FLAVOR}

py-newick Python module to read and write the Newick format

1.10.0 1.9.0Version of this port present on the latest quarterly branch.

Maintainer: wen@FreeBSD.org

Port Added: 2024-02-03 01:00:13

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Also Listed In: python

License: APACHE20

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}newick>0:biology/py-newick@${PY_FLAVOR}

py-ont-fast5-api Interface to HDF5 files in Oxford Nanopore .fast5 format

4.0.2_2 4.0.2_1Version of this port present on the latest quarterly branch.

Maintainer: jwb@FreeBSD.org

Port Added: 2021-08-13 13:36:06

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Also Listed In: python

License: MPL20

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}ont-fast5-api>0:biology/py-ont-fast5-api@${PY_FLAVOR}

py-orange3-bioinformatics Orange add-on providing common functionality for bioinformatics

4.8.4_1 4.3.1_3Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2018-06-14 06:26:12

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Also Listed In: python

License: GPLv3

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}orange3-bioinformatics>0:biology/py-orange3-bioinformatics@${PY_FLAVOR}