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test-nginx01 & pg02
Category listing - biology
Click to add this to your default watch list[s] Software related to biology.- Number of ports in this category: 171

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


Result Page: 1  2   Next
psi88 Plotting wavefunctions (molecular orbitals) in 3D
1.0_12 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
License: not specified in port
py-Genesis-PyAPI API for the Genesis platform for genetics information processing
1.2.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 13 Jun 2018 01:46:32
Also Listed In: python
License: APACHE20
py-biom-format Biological Observation Matrix (BIOM) Format Project
2.1.6_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 09 May 2016 16:37:53
Also Listed In: python
License: BSD3CLAUSE
py-biopython Collection of Python modules for bioinformatics
1.71_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: mauricio@arareko.net search for ports maintained by this maintainer
Port Added: 31 Jul 2000 09:12:24
Also Listed In: python
License: BSD3CLAUSE
py-bx-python Python module for reading, manipulating and writing genomic data sets
0.8.1_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 02 Dec 2017 20:46:35
Also Listed In: python
License: BSD3CLAUSE
py-orange3-bioinformatics Orange add-on providing common functionality for bioinformatics
3.1.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 14 Jun 2018 06:26:10
Also Listed In: python
License: GPLv3
py-pymol OpenGL-based molecular visualization system
2.1.0_2* search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 19 Dec 2017 19:49:25
Also Listed In: science python
License: PyMOL
py-pysam Python module for reading, manipulating and writing genomic data sets
0.14.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 06 May 2017 06:30:42
Also Listed In: python
License: MIT
pycogent Toolkit for statistical analysis of biological sequences
1.9_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: python@FreeBSD.org search for ports maintained by this maintainer
Port Added: 22 Jun 2009 12:47:26
Also Listed In: python
License: GPLv2
pyfasta Fast, memory-efficient, pythonic access to fasta sequence files
0.5.2_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 18 Nov 2009 05:53:48
Also Listed In: python
License: MIT
python-nexus Generic nexus file format reader for python
1.61 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 29 Dec 2009 13:39:49
Also Listed In: python
License: BSD3CLAUSE
rainbow Efficient clustering and assembling of short reads, especially for RAD
2.0.4 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 02 Apr 2018 16:50:56
License: GPLv3+
raster3d Set of tools for generating raster images of proteins and molecules
3.0.2_11* search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 28 Apr 2006 14:21:11
Also Listed In: graphics
License: ART20
recombine Program to fit population models across sites
1.41 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 06 Aug 2001 11:49:53
License: not specified in port
ruby-bio Integrated environment for Bioinformatics written in Ruby
1.5.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: mauricio@arareko.net search for ports maintained by this maintainer
Port Added: 24 Oct 2001 03:21:52
Also Listed In: ruby
License: GPLv2 RUBY
rubygem-bio Integrated environment for Bioinformatics written in Ruby
1.5.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: ruby@FreeBSD.org search for ports maintained by this maintainer
Port Added: 05 Feb 2017 04:27:03
Also Listed In: rubygems
License: BSD2CLAUSE RUBY
samtools Tools for manipulating next-generation sequencing data
1.6 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: cartwright@asu.edu search for ports maintained by this maintainer
Port Added: 15 Dec 2014 21:59:37
License: MIT
seaview Multiple DNA/protein sequence alignment editor
4.6.5,1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: bofh@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
License: GPLv3
seqan C++ sequence analysis template library
2.4.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: h2+fbsdports@fsfe.org search for ports maintained by this maintainer
Port Added: 06 Jun 2012 17:52:27
License: BSD3CLAUSE
seqan-apps Official bioinformatic applications based on the SeqAn library
2.4.0_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: h2+fbsdports@fsfe.org search for ports maintained by this maintainer
Port Added: 10 May 2016 00:52:12
License: BSD3CLAUSE LGPL3 GPLv3
seqan1 C++ Sequence Analysis Library
1.3.1_4 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: h2+fbsdports@fsfe.org search for ports maintained by this maintainer
Port Added: 10 May 2016 01:05:34
License: BSD3CLAUSE
seqio Set of C functions which can read/write biological sequence files
1.2.2_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 22 Aug 2001 09:07:26
License: not specified in port
seqtk Tool for processing sequences in FASTA/FASTQ format
1.2.8 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 03 Apr 2018 20:57:19
License: GPLv2
seqtools Tools for visualising sequence alignments
4.44.1_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: pi@FreeBSD.org search for ports maintained by this maintainer
Port Added: 10 Nov 2013 11:01:14
License: GPLv3
sim4 Algorithm for aligning expressed DNA with genomic sequences
2003.09.21_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 27 Jul 2000 11:33:01
License: GPLv2
slclust Single-linkage clustering with Jaccard similarity
2010.02.02 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 23 Mar 2016 11:00:52
License: ART10
smithwaterman Smith-waterman-gotoh alignment algorithm
g20160702 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 15 Apr 2018 17:46:20
License: GPLv2
stacks Software pipeline for building loci from short-read sequences
1.48 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 31 Mar 2018 13:16:34
License: GPLv2
stringtie Transcript assembly and quantification for RNA-seq
1.3.4.d search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: mzaki@niid.go.jp search for ports maintained by this maintainer
Port Added: 11 Jul 2018 21:32:57
License: ART20 MIT
tRNAscan-SE Searching for tRNA genes in genomic sequence
2.0.0_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Broken BROKEN: missing plist
Ignore IGNORE: is marked as broken: missing plist
Maintainer: mzaki@niid.go.jp search for ports maintained by this maintainer
Port Added: 27 Mar 2002 14:19:04
License: GPLv3+
t_coffee Multiple DNA or protein sequence alignment package
9.03_7 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 25 Jan 2002 11:58:16
License: GPLv2
tabixpp C++ wrapper to tabix indexer
1.0.0.10 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 14 Apr 2018 23:52:29
License: MIT
tinker General purpose molecular modelling package
7.1.3_4 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Restricted RESTRICTED: author requests no distribution except from his FTP site

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
License: tinker
treepuzzle Maximum likelihood phylogeny reconstruction using quartets
5.2 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jan.lentfer@web.de search for ports maintained by this maintainer
Port Added: 20 Nov 2002 09:04:07
License: not specified in port
trimadap Trim adapter sequences from Illumina data using heuristic rules
0.1.3 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 03 Apr 2018 18:24:21
License: GPLv2
trimmomatic Flexible read trimming tool for Illumina NGS data
0.35 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 17 Mar 2016 08:21:26
Also Listed In: java
License: GPLv3
ugene Free, open-source, cross-platform bioinformatics toolkit
1.22.0_3 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: h2+fbsdports@fsfe.org search for ports maintained by this maintainer
Port Added: 23 Feb 2013 04:51:12
Also Listed In: science
License: GPLv2
unanimity Pacific Biosciences consensus library and applications
g20180307 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 24 Apr 2018 14:17:02
License: BSD3CLAUSE
vcflib C++ library and CLI tools for parsing and manipulating VCF files
1.0.0.r1.130 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 17 Apr 2018 03:11:48
License: MIT
vcftools Tools for working with VCF genomics files
0.1.15 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 26 Feb 2016 17:08:07
License: LGPL3
velvet Sequence assembler for very short reads
1.2.10_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 07 Nov 2009 01:24:24
License: not specified in port
wise Intelligent algorithms for DNA searches
2.4.1_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 10 Sep 2002 13:59:05
License: not specified in port
xmolwt Calculate atom weight and percent of each element for a given formula
0.7_7 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
License: not specified in port

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