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

InsightToolkit Insight Toolkit
4.11.0^*

Maintainer: woodsb02@FreeBSD.org
Port Added: 15 Apr 2017 03:04:29
Also Listed In: science
License: APACHE20

InsightToolkit Insight Toolkit
4.12.0^*

Maintainer: woodsb02@FreeBSD.org
Port Added: 07 Sep 2006 03:14:06
Also Listed In: science
License: APACHE20

afni Advanced Functional Neuro Imaging
2015.11.13_4^*

Maintainer: bacon4000@gmail.com
Port Added: 25 Jan 2006 17:37:44
Also Listed In: science graphics
License: GPLv2

ariadne Programs to compare protein sequences and profiles
1.3

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: 22 Jun 2004 14:31:00
License: not specified in port

artemis DNA sequence viewer and annotation tool
9_2

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: 22 Dec 2001 11:39:40
Also Listed In: java
License: not specified in port

avida Auto-adaptive genetic system designed for ALife research
2.12.4

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: 20 Apr 2002 15:17:56
License: GPLv3

babel Converts among various molecular file formats
1.6_4

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
Also Listed In: converters
License: not specified in port

bcftools Tools for manipulating next-generation sequencing data
1.3.1_1

Maintainer: cartwright@asu.edu
Port Added: 05 Jun 2015 21:01:24
License: GPLv3

bedtools Toolset for genome arithmetic
2.25.0

Maintainer: scottcheloha@gmail.com
Port Added: 19 Jan 2016 08:56:42
License: GPLv2

biococoa Bioinformatics framework
2.2.2_2

Maintainer: theraven@FreeBSD.org
Port Added: 30 Dec 2006 09:21:22
Also Listed In: gnustep
License: LGPL21

biojava Open-source Java tools for processing biological data
1.7,1

BROKEN: Does not build
IGNORE: is marked as broken: Does not build

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: 10 Oct 2000 08:14:04
Also Listed In: java
License: not specified in port

blat Fast tool for local sequence similarity searches
36

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: 15 Mar 2006 10:29:12
License: NONE

bowtie Ultrafast, memory-efficient short read aligner
1.1.2_3

Maintainer: bacon4000@gmail.com
Port Added: 05 Mar 2016 13:21:35
License: ART10

bowtie Ultrafast, memory-efficient short read aligner
1.1.2_2

Maintainer: bacon4000@gmail.com
Port Added: 02 Apr 2017 09:09:14
License: ART10

bowtie2 Ultrafast, memory-efficient short read aligner
2.3.0_1

Maintainer: bacon4000@gmail.com
Port Added: 23 Mar 2016 11:22:47
License: GPLv3+

bwa Burrows-Wheeler sequence aligner
0.7.9a

Maintainer: bacon4000@gmail.com
Port Added: 25 Sep 2015 18:39:48
License: GPLv3

cd-hit Clustering and comparing protein or nucleotide sequences
4.6.6_1

Maintainer: bacon4000@gmail.com
Port Added: 02 Apr 2017 09:09:14
License: GPLv2

cd-hit Clustering and comparing protein or nucleotide sequences
4.6.6_1

Maintainer: bacon4000@gmail.com
Port Added: 19 Sep 2015 11:17:00
License: GPLv2

cdbfasta Fast indexing and retrieval of FASTA records from flat file databases
2010.07.22

Maintainer: bacon4000@gmail.com
Port Added: 25 Sep 2015 18:37:34
License: not specified in port

chemeq Outputs LaTeX code for chemical reaction
1.50_2

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: 10 Jul 2000 00:14:19
Also Listed In: textproc
License: GPLv2

clustalw Multiple alignment program for DNA or proteins
2.1_1

RESTRICTED: No commercial use.

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: 10 Jul 2000 00:17:41
License: not specified in port

consed Graphical tool for editing Phrap assemblies
27.0

RESTRICTED: Redistribution is not permitted in any form. You must request access permission via e-mail to get the tarball. Free for academic use.
Maintainer: mzaki@m.u-tokyo.ac.jp
Port Added: 24 May 2008 07:01:28
License: not specified in port

crux Software toolkit for phylogenetic inference
1.2.0_7

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: 08 Jun 2009 23:51:06
Also Listed In: python
License: BSD2CLAUSE BSD3CLAUSE

crux Software toolkit for phylogenetic inference
1.2.0_7

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: 02 Apr 2017 09:09:14
Also Listed In: python
License: BSD2CLAUSE BSD3CLAUSE

cycle Calendar program for women
0.3.1_10^*

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: 30 Jun 2005 14:05:46
Also Listed In: deskutils python
License: GPLv2+

diamond BLAST-compatible local sequence aligner
0.9.8

Maintainer: jrm@FreeBSD.org
Port Added: 06 May 2016 08:45:09
License: AGPLv3

diamond BLAST-compatible local sequence aligner
0.8.36_1

Maintainer: jrm@FreeBSD.org
Port Added: 02 Apr 2017 09:09:14
License: BSD3CLAUSE

emboss Collection of open source tools for genetic sequence analysis
6.6.0_3

Maintainer: wen@FreeBSD.org
Port Added: 31 Jul 2000 16:13:54
License: GPLv2

fasta Collection of programs for searching DNA and protein databases
21.1.1

NO CDROM: May not be sold or incorporated into a commercial product

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: 11 Feb 2001 13:24:20
License: not specified in port

fasta3 Collection of programs for searching DNA and protein databases
36.3.8

NO CDROM: May not be sold or incorporated into a commercial product
Maintainer: wendell@bsd.com.br
Port Added: 11 Feb 2001 13:29:00
License: Fasta

fastdnaml Faster DNAML, makes phylogenetic trees using maximum likelihood
1.2.2_2

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: 12 Oct 2000 09:31:14
License: GPLv2+

fastool Simple and quick FastQ and FastA tool for file reading and conversion
0.1.4

Maintainer: bacon4000@gmail.com
Port Added: 25 Sep 2015 18:35:23
License: BSD2CLAUSE

fasttree Approximately-maximum-likelihood phylogenetic trees from alignments
2.1.8_2

Maintainer: bacon4000@gmail.com
Port Added: 02 Apr 2017 09:09:14
License: not specified in port

fasttree Approximately-maximum-likelihood phylogenetic trees from alignments
2.1.8_2

Maintainer: bacon4000@gmail.com
Port Added: 25 Sep 2015 18:34:35
License: not specified in port

fastx-toolkit CLI tools for Short-Reads FASTA/FASTQ files preprocessing
0.0.14

Maintainer: bacon4000@gmail.com
Port Added: 25 Sep 2015 18:33:28
License: AGPLv3+

fluctuate Program to fit population models
1.40

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: 06 Aug 2001 11:45:39
License: not specified in port

garlic Molecular viewer, editor, and visualization program
1.6_1

Maintainer: maho@FreeBSD.org
Port Added: 28 Jul 2003 06:41:18
License: not specified in port

gff2ps Converts gff-formated genomic data-sets to PostScript
0.98d_2

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: 19 Dec 2001 07:03:28
License: GPLv2+

gmap Genomic Mapping and Alignment Program for mRNA and EST Sequences
2015.09.21

Maintainer: bacon4000@gmail.com
Port Added: 29 Sep 2006 04:09:50
License: GMAP

gperiodic Displays a periodic table of the elements
2.0.10_8

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
License: GPLv2+

grappa Genome Rearrangements Analysis and Phylogeny Software
2.0

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: 04 Jul 2001 05:39:40
License: GPLv2

hmmer Profile hidden Markov models for biological sequence analysis
3.0_1

Maintainer: bacon4000@gmail.com
Port Added: unknown
License: GPLv3

htslib C library for high-throughput sequencing data formats
1.3.1

Maintainer: cartwright@asu.edu
Port Added: 14 Dec 2014 22:35:26
Also Listed In: devel
License: BSD3CLAUSE MIT

iolib General purpose trace file (and Experiment File) reading interface
1.14.9

Maintainer: danilo@FreeBSD.org
Port Added: 28 Aug 2009 23:34:46
License: BSD3CLAUSE

jalview Viewer and editor for multiple sequence alignments
2.07_2

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: 13 Feb 2006 09:43:01
Also Listed In: java
License: not specified in port

jellyfish Fast, memory-efficient counting of k-mers in DNA
2.2.6_1

Maintainer: bacon4000@gmail.com
Port Added: 24 Mar 2016 13:53:24
License: GPLv3+

jellyfish Fast, memory-efficient counting of k-mers in DNA
2.2.6_1

Maintainer: bacon4000@gmail.com
Port Added: 02 Apr 2017 09:09:14
License: GPLv3+

lagan Efficient tools for large-scale multiple alignments of genomic DNA
2.0_1

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: 16 Mar 2006 22:31:50
License: GPLv2

lamarc Package of programs for computing population parameters
2.1.8_1,1

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: 07 Aug 2001 05:17:58
License: APACHE20

libgtextutils Gordon's text utilities
0.7

Maintainer: bacon4000@gmail.com
Port Added: 25 Sep 2015 18:31:38
License: AGPLv3

libsbml API Library for Working with SBML File
5.15.0

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: 28 May 2009 23:36:42
Also Listed In: devel
License: LGPL21

linux-foldingathome Distributed client for Protein Folding
5.04

Maintainer: onatan@gmail.com
Port Added: 28 Aug 2006 22:34:01
License: not specified in port

mafft Multiple alignment program for amino acid or nucleotide sequences
7.266

Maintainer: cartwright@asu.edu
Port Added: 15 Mar 2006 10:41:45
License: BSD2CLAUSE

mapm3 Constructs linkage maps of markers segregating in experimental crosses
3.0

Maintainer: tphilipp@potion-studios.com
Port Added: 06 Apr 2008 04:49:23
License: not specified in port

migrate Program to estimate population sizes and migration rates
3.6.11

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: 06 Aug 2001 10:07:46
License: not specified in port

minc2 Medical Imaging NetCDF
2.2.00_5,1^*

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: 30 Apr 2006 12:09:06
Also Listed In: science
License: MIT

molden Display molecular orbitals and electron densities in 2D and 3D
5.7_4,1

BROKEN: does not fetch, size/checksum mismatch
IGNORE: is marked as broken: does not fetch, size/checksum mismatch
RESTRICTED: free for academic, non profit usage; do not re-distribute source and executable.
Maintainer: pi@FreeBSD.org
Port Added: 07 Feb 2017 14:21:17
License: Molden

molden Display molecular orbitals and electron densities in 2D and 3D
5.7_2,1

RESTRICTED: free for academic, non profit usage; do not re-distribute source and executable.
Maintainer: pi@FreeBSD.org
Port Added: 11 Nov 2016 06:09:22
License: Molden

molden Display molecular orbitals and electron densities in 2D and 3D
5.7_8,1

BROKEN: Fails to fetch
IGNORE: is marked as broken: Fails to fetch
RESTRICTED: free for academic, non profit usage; do not re-distribute source and executable.
Maintainer: jmd@FreeBSD.org
Port Added: unknown
License: Molden

molden Display molecular orbitals and electron densities in 2D and 3D
5.7_6,1

RESTRICTED: free for academic, non profit usage; do not re-distribute source and executable.
Maintainer: jmd@FreeBSD.org
Port Added: 02 Apr 2017 09:09:14
License: Molden

mopac Semi-empirical (MNDO, etc.) molecular orbital calculation
7.1.15_2,1

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
License: GPLv2+

mopac Semi-empirical (MNDO, etc.) molecular orbital calculation
7.1.15_2,1

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: 02 Apr 2017 09:09:14
License: GPLv2+

mrbayes Bayesian inference of phylogeny
3.1.2_1

Maintainer: mzaki@m.u-tokyo.ac.jp
Port Added: 15 Dec 2007 15:13:49
License: not specified in port

mummer Modular system for rapid whole genome alignment
3.23_1

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: 14 Dec 2007 20:56:11
License: not specified in port

muscle MUltiple Sequence Comparison by Log-Expectation
3.8.31

Maintainer: mzaki@m.u-tokyo.ac.jp
Port Added: 14 May 2008 13:52:50
License: not specified in port

ncbi-blast+ NCBI implementation of Basic Local Alignment Search Tool
2.5.0_1

Maintainer: bacon4000@gmail.com
Port Added: 02 Apr 2017 09:09:14
License: PD

ncbi-blast+ NCBI implementation of Basic Local Alignment Search Tool
2.5.0_1

Maintainer: bacon4000@gmail.com
Port Added: 30 Dec 2014 20:03:26
License: PD

ncbi-toolkit NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
2012.06.20_1

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: 29 Oct 2000 10:56:24
License: not specified in port

njplot Phylogenetic tree drawing program
2.4

Maintainer: jrm@FreeBSD.org
Port Added: 14 May 2008 14:07:25
License: NONE

p5-AcePerl Perl5 interface to the ACEDB genome database system
1.92_5

Maintainer: perl@FreeBSD.org
Port Added: 28 Jul 2000 10:16:10
Also Listed In: databases perl5
License: ART10 GPLv1

p5-Bio-ASN1-EntrezGene Regular expression-based Perl Parser for NCBI Entrez Gene
1.72_1,1

Maintainer: perl@FreeBSD.org
Port Added: 15 Oct 2005 20:11:03
Also Listed In: perl5
License: ART10 GPLv1

p5-Bio-Coordinate Modules for working with biological coordinates
1.007001

Maintainer: sunpoet@FreeBSD.org
Port Added: 19 Dec 2016 16:00:37
Also Listed In: perl5
License: ART10 GPLv1

p5-Bio-Das Client-side library for Distributed Genome Annotation System
1.17_4

Maintainer: perl@FreeBSD.org
Port Added: 01 Sep 2005 13:10:39
Also Listed In: perl5
License: ART10 GPLv1

p5-Bio-Das-Lite Perl extension for the DAS (HTTP+XML) Protocol
2.11_1

Maintainer: perl@FreeBSD.org
Port Added: 01 Mar 2010 09:16:56
Also Listed In: perl5
License: ART10 GPLv1

p5-Bio-GFF3 Fast low-level functions for parsing and formatting GFF3
2.0_2

Maintainer: perl@FreeBSD.org
Port Added: 22 Apr 2011 08:51:49
Also Listed In: perl5
License: ART10 GPLv1

p5-Bio-Glite Perl Interface to G-language
0.10_2

Maintainer: perl@FreeBSD.org
Port Added: 02 Apr 2009 18:25:38
Also Listed In: perl5
License: not specified in port

p5-Bio-Graphics Generate GD Images of Bio::Seq Objects
2.40_2

Maintainer: perl@FreeBSD.org
Port Added: 10 Mar 2009 18:52:27
Also Listed In: perl5
License: ART10 GPLv1

p5-Bio-MAGETAB Data model and utility API for the MAGE-TAB format
1.31_1

Maintainer: perl@FreeBSD.org
Port Added: 01 Jul 2009 09:03:56
Also Listed In: perl5
License: GPLv2

p5-Bio-NEXUS Object-oriented Perl API for the NEXUS file format
0.78_1

Maintainer: perl@FreeBSD.org
Port Added: 22 Aug 2009 20:40:26
Also Listed In: perl5
License: not specified in port

p5-Bio-Phylo Phylogenetic analysis using Perl
0.58_1

Maintainer: perl@FreeBSD.org
Port Added: 13 May 2006 16:50:16
Also Listed In: perl5
License: ART10 GPLv1

p5-Bio-SCF Read and Update SCF Chromatographic Sequence Files
1.03_1

Maintainer: wen@FreeBSD.org
Port Added: 28 Aug 2009 23:38:55
Also Listed In: perl5
License: not specified in port

p5-BioPerl Collection of Perl modules for bioinformatics
1.007001_2

Maintainer: perl@FreeBSD.org
Port Added: 18 Dec 2016 15:27:08
Also Listed In: perl5
License: ART10 GPLv1

p5-BioPerl-Run Wrapper modules for common bioinformatics tools
1.007001_1

Maintainer: perl@FreeBSD.org
Port Added: 18 Dec 2016 15:29:01
Also Listed In: perl5
License: ART10 GPLv1

p5-transdecoder Identify candidate coding regions within transcript sequences
2.1.0

Maintainer: bacon4000@gmail.com
Port Added: 16 Mar 2016 20:12:42
Also Listed In: perl5
License: BSD3CLAUSE

paml Phylogenetic Analysis by Maximum Likelihood (PAML)
4.9c_1

Maintainer: jrm@FreeBSD.org
Port Added: 10 Jul 2000 00:21:06
License: GPLv3

phrap Phrap is a program for assembling shotgun DNA sequence data
1.090518

IGNORE: you must request the source code \(distrib.tar.gz\) via e-mail, place it manually in /usr/local/PORTS-head/distfiles/phrap, and then try it again
RESTRICTED: Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.
Maintainer: mzaki@m.u-tokyo.ac.jp
Port Added: 24 May 2008 07:03:43
License: not specified in port

phred Base calling and quality value assignment on DNA sequencing
0.020425.c

RESTRICTED: Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.
Maintainer: mzaki@m.u-tokyo.ac.jp
Port Added: 24 May 2008 07:05:09
License: not specified in port

phylip Phylogeny Inference Package
3.696,1

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: 10 Jul 2000 00:25:48
License: BSD2CLAUSE

phyml Simple, fast, and accurate algorithm to estimate large phylogenies
3.2.0,1

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: 21 Jul 2009 01:10:33
License: GPLv2

plink Whole genome association analysis toolset
1.07_6

Maintainer: bacon4000@gmail.com
Port Added: 27 Sep 2012 10:00:09
Also Listed In: science
License: GPLv2

plink Whole genome association analysis toolset
1.07_6

Maintainer: bacon4000@gmail.com
Port Added: 02 Apr 2017 09:09:14
Also Listed In: science
License: GPLv2

plinkseq Toolset for working with human genetic variation data
0.10_1

Maintainer: bacon4000@gmail.com
Port Added: 27 Sep 2012 10:00:09
Also Listed In: science
License: GPLv2

primer3 Primer3 helps to choose primers for PCR reactions
2.3.6

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: 17 Sep 2002 15:31:31
License: GPLv2

protomol OO, component based, framework for molecular dynamics (MD) simulations
2.0.3_13

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: 05 May 2006 20:12:57
License: GPLv2

psi88 Plotting wavefunctions (molecular orbitals) in 3D
1.0_10

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: 02 Apr 2017 09:09:14
License: not specified in port

psi88 Plotting wavefunctions (molecular orbitals) in 3D
1.0_10

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
License: not specified in port

py-biom-format Biological Observation Matrix (BIOM) Format Project
2.1.6

Maintainer: jrm@FreeBSD.org
Port Added: 09 May 2016 16:37:53
Also Listed In: python
License: BSD3CLAUSE

py-biopython Collection of Python modules for bioinformatics
1.69

Maintainer: mauricio@arareko.net
Port Added: 31 Jul 2000 09:12:24
Also Listed In: python
License: not specified in port

py-bx-python Python module for reading, manipulating and writing genomic data sets
0.7.4

Maintainer: yuri@rawbw.com
Port Added: 06 May 2017 06:28:34
Also Listed In: python
License: MIT

py-pysam Python module for reading, manipulating and writing genomic data sets
0.11.2.2

Maintainer: yuri@rawbw.com
Port Added: 06 May 2017 06:30:42
Also Listed In: python
License: MIT

13 vulnerabilities affecting 73 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities