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

InsightToolkit Insight Toolkit
4.13.0_2^*

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

MOOSE-neural-simulator Multiphysics Object Oriented Simulation Environment
3.1.2_1^*

Maintainer: yuri@FreeBSD.org
Port Added: 19 Dec 2017 16:04:41
Also Listed In: science
License: GPLv3

afni Advanced Functional Neuro Imaging
2015.11.13_6^*

Maintainer: jwb@FreeBSD.org
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

BROKEN: No public distfiles
IGNORE: is marked as broken: No public distfiles

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

bamtools API and toolkit for handling BAM files
2.5.1

Maintainer: jwb@FreeBSD.org
Port Added: 28 Mar 2018 13:26:48
License: MIT

bcftools Tools for manipulating next-generation sequencing data
1.6

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

bedtools Toolset for genome set arithmetic such as intersect, union
2.27.1

Maintainer: jwb@FreeBSD.org
Port Added: 19 Jan 2016 08:56:42
License: GPLv2

biococoa Bioinformatics framework
2.2.2_4

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

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_5

Maintainer: jwb@FreeBSD.org
Port Added: 05 Mar 2016 13:21:35
License: ART10

bowtie2 Ultrafast, memory-efficient short read aligner
2.3.3.1

Maintainer: jwb@FreeBSD.org
Port Added: 23 Mar 2016 11:22:47
License: GPLv3+

bwa Burrows-Wheeler sequence aligner
0.7.17

Maintainer: jwb@FreeBSD.org
Port Added: 25 Sep 2015 18:39:48
License: GPLv3

canu Single molecule sequence assembler
1.6_3

Maintainer: jwb@FreeBSD.org
Port Added: 22 Dec 2017 01:30:37
Also Listed In: java perl5
License: GPLv2

cd-hit Clustering and comparing protein or nucleotide sequences
4.6.6_3

Maintainer: jwb@FreeBSD.org
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: jwb@FreeBSD.org
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_9

BROKEN: No public distfiles
IGNORE: is marked as broken: No public distfiles

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

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+

ddocent Bash pipeline for RAD sequencing
2.2.25

Maintainer: jwb@FreeBSD.org
Port Added: 20 Apr 2018 01:34:22
Also Listed In: java
License: MIT

diamond BLAST-compatible local sequence aligner
0.9.21

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

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

fastahack Utility for indexing and sequence extraction from FASTA files
g20160702

Maintainer: jwb@FreeBSD.org
Port Added: 16 Apr 2018 14:50:59
License: GPLv2

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: jwb@FreeBSD.org
Port Added: 25 Sep 2015 18:35:23
License: BSD2CLAUSE

fastqc Quality control tool for high throughput sequence data
0.11.5

Maintainer: jwb@FreeBSD.org
Port Added: 30 Nov 2017 22:54:38
Also Listed In: java perl5
License: GPLv3

fasttree Approximately-maximum-likelihood phylogenetic trees from alignments
2.1.10_1

Maintainer: jwb@FreeBSD.org
Port Added: 25 Sep 2015 18:34:35
License: GPLv2+

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

Maintainer: jwb@FreeBSD.org
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

freebayes Bayesian haplotype-based polymorphism discovery and genotyping
1.2.0

Maintainer: jwb@FreeBSD.org
Port Added: 20 Apr 2018 00:07:39
License: MIT

garlic Molecular viewer, editor, and visualization program
1.6_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: 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: jwb@FreeBSD.org
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
3.1b2

Maintainer: mzaki@niid.go.jp
Port Added: unknown
License: GPLv3

htslib C library for high-throughput sequencing data formats
1.6

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

iqtree Efficient phylogenomic software by maximum likelihood
1.6.3

Maintainer: jrm@FreeBSD.org
Port Added: 21 Oct 2017 16:58:02
License: GPLv2

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_2

Maintainer: jwb@FreeBSD.org
Port Added: 24 Mar 2016 13:53:24
License: GPLv3+

kallisto Quantify abundances of transcripts from RNA-Seq data
0.43.1

Maintainer: jwb@FreeBSD.org
Port Added: 02 Dec 2017 20:44:35
License: BSD2CLAUSE

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: jwb@FreeBSD.org
Port Added: 25 Sep 2015 18:31:38
License: AGPLv3

libsbml API Library for Working with SBML File
5.16.0

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_6,1^*

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_14,1

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

mopac Semi-empirical (MNDO, etc.) molecular orbital calculation
7.1.15_4,1

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+

mrbayes Bayesian inference of phylogeny
3.1.2_2

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_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: 14 Dec 2007 20:56:11
License: ART10

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
2.7.1

Maintainer: jwb@FreeBSD.org
Port Added: 30 Dec 2014 20:03:26
Also Listed In: perl5 python
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-FeatureIO Handler for FeatureIO
1.6.905

Maintainer: sunpoet@FreeBSD.org
Port Added: 15 Sep 2017 19:17:29
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
2.0.1

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
1.007002

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
1.007002

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

p5-TrimGalore Wrapper around Cutadapt and FastQC for adapter and quality trimming
0.4.5

Maintainer: jwb@FreeBSD.org
Port Added: 09 Dec 2017 13:23:40
Also Listed In: perl5
License: GPLv3

p5-transdecoder Identify candidate coding regions within transcript sequences
2.1.0_1

Maintainer: jwb@FreeBSD.org
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

pbseqan Pacific Biosciences patched and stripped down SeqAn
g20171002

Maintainer: jwb@FreeBSD.org
Port Added: 21 Apr 2018 17:21:58
License: BSD3CLAUSE

pear-merger Memory-efficient and highly accurate paired-end read merger
0.9.6

Maintainer: jwb@FreeBSD.org
Port Added: 04 Apr 2018 17:21:55
License: CC-BY-NC-SA-3.0

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 /var/db/repos/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
3.697,1

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
3.3.20180129,1

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_8

BROKEN: no public distfiles
IGNORE: is marked as broken: no public distfiles
Maintainer: jwb@FreeBSD.org
Port Added: 27 Sep 2012 10:00:09
Also Listed In: science
License: GPLv2

plinkseq Toolset for working with human genetic variation data
0.10_1

Maintainer: jwb@FreeBSD.org
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_12

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_2

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
1.71

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
0.8.1_1

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

py-cutadapt Finds and removes adapter sequences, primers, poly-A tails, etc
1.14

Maintainer: jwb@FreeBSD.org
Port Added: 29 Nov 2017 22:17:53
Also Listed In: python
License: MIT

py-macs2 Analysis of chromatin immunoprecipitation (ChIP) sequences
2.1.0.p20170505_1

Maintainer: jwb@FreeBSD.org
Port Added: 02 Dec 2017 20:46:35
Also Listed In: python
License: BSD3CLAUSE

py-pymol OpenGL-based molecular visualization system
2.1.0_1^*

Maintainer: yuri@FreeBSD.org
Port Added: 19 Dec 2017 19:49:25
Also Listed In: science python
License: PyMOL

13 vulnerabilities affecting 120 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities

Last updated:
2018-04-21 10:09:45